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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
2AH4
guanidinobenzoyl-trypsin acyl-enzyme at 1.13 A resolution
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 (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
5
Temperature
298.0
Details
ammonium sulfate, bis-tris propane, calcium chloride, 4-nitrophenyl 4-guanidinobenzoate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 54.45
α = 90
b = 57.91
β = 90
c = 66.77
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 4
--
2005-04-01
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ALS BEAMLINE 8.3.1
1.00000
ALS
8.3.1
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
1.13
43.85
99.97
0.056
0.056
--
3.5
75171
75171
--
-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)
1.13
1.19
--
0.533
0.533
1.5
1.6
--
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
1.13
43.85
--
0.0
75169
75169
3830
99.97
0.12
0.12
0.119
0.146
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
1.13
1.159
--
186
3475
0.322
0.326
--
--
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
anisotropic
Mean Isotropic B
8.644
Anisotropic B[1][1]
0.81
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
-0.39
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-0.42
RMS Deviations
Key
Refinement Restraint Deviation
r_rigid_bond_restr
5.558
r_chiral_restr
0.148
r_scbond_it
4.63
r_dihedral_angle_4_deg
18.001
r_sphericity_bonded
5.3
r_sphericity_free
13.627
r_bond_refined_d
0.016
r_mcbond_it
2.719
r_dihedral_angle_3_deg
11.903
r_gen_planes_refined
0.01
r_mcbond_other
1.429
r_dihedral_angle_2_deg
40.355
r_nbd_other
0.26
r_nbd_refined
0.364
r_symmetry_vdw_refined
0.279
r_scangle_it
5.931
r_gen_planes_other
0.011
r_metal_ion_refined
0.128
r_angle_refined_deg
1.794
r_mcangle_it
3.563
r_bond_other_d
0.004
r_symmetry_vdw_other
0.282
r_nbtor_other
0.093
r_dihedral_angle_1_deg
6.609
r_xyhbond_nbd_refined
0.211
r_angle_other_deg
2.686
r_symmetry_hbond_refined
0.271
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
1674
Nucleic Acid Atoms
0
Heterogen Atoms
33
Solvent Atoms
359
Software
Software
Software Name
Purpose
MOSFLM
data reduction
SCALA
data scaling
TRUNCATE
data reduction
EPMR
phasing
REFMAC
refinement version: 5.2
CCP4
data scaling version: (SCALA
TRUNCATE
data scaling