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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
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Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4GAW
Crystal structure of active human granzyme H
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
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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+S)
Biological Assembly 2 (gz) (A+S)
Biological Assembly 3 (gz) (A+S)
Biological Assembly 4 (gz) (A+S)
Biological Assembly 5 (gz) (A+S)
Biological Assembly 6 (gz) (A+S)
Biological Assembly 7 (gz) (A+S)
Biological Assembly 8 (gz) (A+S)
Biological Assembly 9 (gz) (A+S)
Biological Assembly 10 (gz) (A+S)
Biological Assembly 11 (gz) (A+S)
Biological Assembly 12 (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
8.5
Temperature
289.0
Details
0.2M Li2SO4, 0.1M Bicine (pH8.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 170.37
α = 90
b = 367.07
β = 90
c = 61.14
γ = 90
Symmetry
Space Group
P 21 21 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315r
--
2009-06-07
Diffraction Radiation
Monochromator
Protocol
Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal)
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-5A
0.9
Photon Factory
BL-5A
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
3
39.8
100.0
0.082
--
--
7.0
78537
78537
0.0
0.0
--
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)
3.0
3.11
100.0
0.314
--
6.3
7.1
--
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
MOLECULAR REPLACEMENT
3.0
39.8
--
--
74438
74302
3931
99.8
--
0.27249
0.27069
0.30593
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
3.0
3.077
--
267
5001
0.389
0.448
--
99.79
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
70.066
Anisotropic B[1][1]
-1.61
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
0.23
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
1.38
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_1_deg
8.554
r_chiral_restr
0.117
r_dihedral_angle_4_deg
19.391
r_bond_refined_d
0.012
r_gen_planes_refined
0.008
r_dihedral_angle_2_deg
37.111
r_angle_refined_deg
1.867
r_dihedral_angle_3_deg
21.053
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
21176
Nucleic Acid Atoms
0
Heterogen Atoms
78
Solvent Atoms
38
Software
Software
Software Name
Purpose
ADSC
data collection version: Quantum
COMO
phasing
REFMAC
refinement version: 5.6.0117
HKL-2000
data reduction
HKL-2000
data scaling