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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4F9Z
Crystal Structure of human ERp27
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly 1 (gz) (A)
Biological Assembly 2 (gz) (A)
Biological Assembly 3 (gz) (A)
Biological Assembly 4 (gz) (A)
Biological Assembly 5 (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
8.5
Temperature
293.0
Details
20% PEG 4000, 150mM sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Method
Vapor Diffusion Hanging Drop
pH
8.5
Temperature
293.0
Details
26% PEG 4000, 125mM sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 57.83
α = 70.45
b = 68.36
β = 88.16
c = 86.78
γ = 64.96
Symmetry
Space Group
P 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
2
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
RAYONIX MX-225
--
2012-01-17
CCD
RAYONIX MX-225
--
2011-09-23
Diffraction Radiation
Monochromator
Protocol
Si-111 crystal
SINGLE WAVELENGTH
Si-111 crystal
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
BESSY BEAMLINE 14.1
--
BESSY
14.1
SYNCHROTRON
BESSY BEAMLINE 14.1
0.91841
BESSY
14.1
Data Collection
Overall
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
R Sym I (Observed)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
2
57.81
95.9
0.178
0.113
--
5.4
54973
72979
-3.0
-3.0
--
High Resolution Shell
Resolution (High)
Resolution (Low)
Percent Possible (All)
R Merge I (Observed)
R-Sym I (Observed)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
2.0
2.11
95.1
--
--
--
--
--
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
SAD
2.2
40.675
--
1.97
54973
54932
1371
96.15
0.1712
0.171
0.1699
0.2169
RANDOM
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
2.2
2.2786
5335
137
5335
0.2412
0.293
--
95.0
X Ray Diffraction
2.2786
2.3699
5313
140
5315
0.2276
0.2686
--
95.0
X Ray Diffraction
2.3699
2.4777
5311
123
5311
0.2161
0.2755
--
96.0
X Ray Diffraction
2.4777
2.6083
5348
129
5348
0.2023
0.2755
--
96.0
X Ray Diffraction
2.6083
2.7717
5357
155
5357
0.1898
0.2662
--
96.0
X Ray Diffraction
2.7717
2.9857
5355
134
5355
0.1876
0.2429
--
96.0
X Ray Diffraction
2.9857
3.286
5342
139
5342
0.17
0.2265
--
96.0
X Ray Diffraction
3.286
3.7612
5394
144
5394
0.1564
0.2103
--
97.0
X Ray Diffraction
3.7612
4.7376
5399
135
5399
0.1265
0.1583
--
97.0
X Ray Diffraction
4.7376
40.6817
5405
135
5405
0.1537
0.1774
--
97.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
9.0635
Anisotropic B[1][2]
-0.3947
Anisotropic B[1][3]
-6.5621
Anisotropic B[2][2]
-4.8668
Anisotropic B[2][3]
-0.2829
Anisotropic B[3][3]
-6.252
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.072
f_angle_d
1.07
f_dihedral_angle_d
15.639
f_bond_d
0.007
f_plane_restr
0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
8685
Nucleic Acid Atoms
0
Heterogen Atoms
92
Solvent Atoms
646
Software
Software
Software Name
Purpose
MxCuBE
data collection
SHELXS
phasing
PHENIX
refinement version: (phenix.refine: 1.7.3_928)
MOSFLM
data reduction
SCALA
data scaling