Mass: 16618.432 Da / Num. of mol.: 3 / Mutation: TRYPSIN PROTEOLYSIS AT R58 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN RHOGDI CDNA LOCUS HUMRH / Plasmid: PGEX2T Gene (production host): HUMAN RHOGDI CDNA, LOCUS HUMRHOGDP M97579 Production host: Escherichia coli (E. coli) / References: UniProt: P52565
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.977 Å / Relative weight: 1
Reflection
Resolution: 2.5→30 Å / Num. obs: 20345 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.4
Reflection shell
Resolution: 2.5→2.59 Å / Redundancy: 11 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 8.7 / % possible all: 95.3
Reflection
*PLUS
Redundancy: 7.9 % / Num. measured all: 161161
Reflection shell
*PLUS
% possible obs: 95.3 %
-
Processing
Software
Name
Version
Classification
X-PLOR
3.843
refinement
X-PLOR
3.843
modelbuilding
SHELX
refinement
SHELX
modelbuilding
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
X-PLOR
3.843
phasing
Refinement
Method to determine structure: MIR WITH ANOMALOUS / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: SELENOMETHIONINE DATA WAS STRONGER AND THEREFORE USED FOR REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.298
1000
5.1 %
SHELLS
Rwork
0.225
-
-
-
obs
0.225
19482
92.8 %
-
Displacement parameters
Biso mean: 23 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.39 Å
0.29 Å
Luzzati d res low
-
8 Å
Luzzati sigma a
0.33 Å
0.3 Å
Refinement step
Cycle: LAST / Resolution: 2.5→8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3427
0
45
191
3663
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.012
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
2
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
27.7
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.76
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
2.94
1.5
X-RAY DIFFRACTION
x_mcangle_it
4.46
2
X-RAY DIFFRACTION
x_scbond_it
5.04
2
X-RAY DIFFRACTION
x_scangle_it
6.99
2.5
LS refinement shell
Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
Rfactor
Num. reflection
% reflection
Rfree
0.401
169
5.2 %
Rwork
0.312
3099
-
obs
-
-
94.1 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PARHCSDX.PRO
TOPHCSDX.PRO
X-RAY DIFFRACTION
2
EXTRAPARA.PRO
EXTRATOP.PRO
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi