X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.22 α = 90
b = 48.22 β = 90
c = 63.28 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER APEX II multi-layer optics 2005-01-20
Diffraction Radiation
Monochromator Protocol
GE111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
1.75 17.98 99.8 0.0301 0.0199 -- 10.6 14741 14710 0.0 0.0 33.1
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)
1.75 1.84 99.3 0.2839 0.2574 4.05 3.43 2016

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 1.8 17.0 0.0 0.0 13483 12753 1272 94.61 0.23 0.203 0.198 0.255 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 1.8 1.846 1091 98 749 0.251 0.383 -- 85.3
X Ray Diffraction 1.846 1.896 1030 66 -- 0.232 0.31 -- 87.241
X Ray Diffraction 1.896 1.95 1027 94 -- 0.198 0.255 -- 89.496
X Ray Diffraction 1.95 2.01 979 83 -- 0.218 0.327 -- 91.183
X Ray Diffraction 2.01 2.075 949 78 -- 0.215 0.299 -- 93.915
X Ray Diffraction 2.075 2.146 934 76 -- 0.206 0.284 -- 94.639
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.909
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 7.239
r_scbond_it 5.07
r_mcangle_it 3.159
r_mcbond_it 2.056
r_gen_planes_refined 0.005
r_chiral_restr 0.157
r_dihedral_angle_4_deg 20.903
r_dihedral_angle_3_deg 18.093
r_dihedral_angle_2_deg 29.248
r_dihedral_angle_1_deg 7.47
r_angle_refined_deg 2.08
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1007
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 73

Software

Computing
Computing Package Purpose
APEX Data Collection
SAINT Data Reduction (intensity integration)
SAINT Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0017 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 version: 5.5.0017 refinement
DM version: 6.0.99d density modification
Phaser molecular replacement
SAINT data processing
SAINT collection/data indexing