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- PDB-1zag: HUMAN ZINC-ALPHA-2-GLYCOPROTEIN -

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Basic information

Entry
Database: PDB / ID: 1zag
TitleHUMAN ZINC-ALPHA-2-GLYCOPROTEIN
ComponentsPROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
KeywordsLIPID MOBILIZATION FACTOR / SECRETED MHC CLASS I HOMOLOG
Function / homology
Function and homology information


Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / protein transmembrane transporter activity / RNA nuclease activity / collagen-containing extracellular matrix / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space ...Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / protein transmembrane transporter activity / RNA nuclease activity / collagen-containing extracellular matrix / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Zinc-alpha-2-glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.8 Å
AuthorsChirino, A.J. / Sanchez, L.M. / Bjorkman, P.J.
Citation
Journal: Science / Year: 1999
Title: Crystal structure of human ZAG, a fat-depleting factor related to MHC molecules.
Authors: Sanchez, L.M. / Chirino, A.J. / Bjorkman, P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Biochemical characterization and crystalization of human Zn-alpha2-glycoprotein, a soluble class I major histocompatibility complex homolog.
Authors: Sanchez, L.M. / Lopez-Otin, C. / Bjorkman, P.J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Complete amino acid sequence of human plasma Zn-alpha 2-glycoprotein and its homology to histocompatibility antigens.
Authors: Araki, T. / Gejyo, F. / Takagaki, K. / Haupt, H. / Schwick, H.G. / Burgi, W. / Marti, T. / Schaller, J. / Rickli, E. / Brossmer, R.
History
DepositionFeb 2, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 31, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 30, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.type / _citation.page_last ..._chem_comp.type / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
B: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
C: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
D: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,60616
Polymers126,7384
Non-polymers5,86812
Water724
1
A: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4444
Polymers31,6841
Non-polymers1,7603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8974
Polymers31,6841
Non-polymers2,2133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5514
Polymers31,6841
Non-polymers8673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7134
Polymers31,6841
Non-polymers1,0293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.600, 131.700, 118.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.163668, 0.986411, -0.014382), (0.985991, -0.164039, -0.030225), (-0.032174, -0.009233, -0.99944)-80.321, 102.344, 161.80299
2given(0.094438, -0.473364, 0.87579), (0.974109, 0.22545, 0.016816), (-0.205407, 0.851527, 0.482399)-35.643, 58.035, -45.192
3given(0.978838, 0.145654, 0.143741), (-0.05323, -0.497012, 0.866109), (0.197594, -0.855432, -0.478741)-28.718, 52.045, 52.045
4given(0.181873, 0.982196, -0.047045), (0.982631, -0.18333, -0.028744), (-0.036857, -0.041, -0.998479)-76.6, 103.893, 165.08099
5given(-0.050255, -0.31941, 0.946283), (0.98123, 0.160833, 0.106399), (-0.186179, 0.933868, 0.305332)-54.278, 52.085, -31.528
6given(0.95691, 0.180068, 0.227814), (-0.161448, -0.322184, 0.932808), (0.241367, -0.929394, -0.27923)-42.122, 30.467, 185.095

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Components

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Protein / Non-polymers , 2 types, 8 molecules ABCD

#1: Protein
PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN) / ZN-ALPHA-2-GLYCOPROTEIN / ZAG


Mass: 31684.404 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P25311
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 12 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG


Type: oligosaccharide / Mass: 1317.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG


Type: oligosaccharide / Mass: 1770.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-1-3-1-4-5/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1_h6-i2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Nonpolymer detailsNO ATTEMPT HAS BEEN MADE TO MODEL OR OTHERWISE TAKE THE UNKNOWN LIGAND'S DENSITY INTO ACCOUNT ...NO ATTEMPT HAS BEEN MADE TO MODEL OR OTHERWISE TAKE THE UNKNOWN LIGAND'S DENSITY INTO ACCOUNT DURING REFINEMENT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 63 %
Crystal growpH: 5
Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION METHOD WITH 30% POLYETHYLENE GLYCOL 2000 MONOMETHYLETHER, 0.2M AMMONIUM ACETATE, AND 0.1M SODIUM ACETATE BUFFER (PH 5.0)
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Details: Sanchez, L.M., (1997) Proc.Nat.Acad.Sci.USA, 94, 4626.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMHEPES1drop
30.02 %1dropNaN3
430 %(w/v)mPEG20001reservoir
50.2 Mammonium acetate1reservoir
60.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 39365 / % possible obs: 95.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 27
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.5 / % possible all: 75.7
Reflection shell
*PLUS
% possible obs: 75.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.4refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1970 5 %RANDOM
Rwork0.229 ---
obs-39118 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.15 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 54.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.84 Å20 Å20 Å2
2--1.92 Å20 Å2
3---6.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8864 0 388 4 9256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.82
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.38
X-RAY DIFFRACTIONx_mcangle_it8.07
X-RAY DIFFRACTIONx_scbond_it8.35
X-RAY DIFFRACTIONx_scangle_it11.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2 / Weight position: 300

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTS8.3450.038
228.5550.035
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.43 163 5.3 %
Rwork0.396 2912 -
obs--75.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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