Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
THE CRYSTALLIZED SEQUENCE CORRESPONDS TO THE HUMAN MENIN ISOFORM 2
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal grow
Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data ...Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 200 mM 0RO, VAPOR DIFFUSION, SITTING DROP, temperature 283K
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Data collection
Diffraction
ID
Crystal-ID
1
1
2
1
Diffraction source
Source
Site
Beamline
ID
SYNCHROTRON
APS
21-ID-D
1
APS
21-ID-F
2
Detector
Type: MARMOSAIC 300 mm CCD / Detector: CCD
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 1.56→39.41 Å / Num. obs: 60554 / % possible obs: 86.4 % / Redundancy: 3.8 % / Rsym value: 0.06 / Net I/σ(I): 25.5
Reflection shell
Resolution: 1.56→1.59 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.686 / % possible all: 92.1
Resolution: 1.56→39.41 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.534 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21412
3036
5 %
RANDOM
Rwork
0.17586
-
-
-
obs
0.17779
57379
86.17 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 24.294 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.56→39.41 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3676
0
62
370
4108
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
3899
X-RAY DIFFRACTION
r_angle_refined_deg
1.666
1.974
5302
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.286
5
482
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.908
23.743
179
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.738
15
649
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.356
15
27
X-RAY DIFFRACTION
r_chiral_restr
0.108
0.2
581
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
2962
LS refinement shell
Resolution: 1.56→1.601 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.284
201
-
Rwork
0.259
4145
-
obs
-
-
89.09 %
+
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