X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 291.0
Details 0.2M imidazole malate, 5% glycerol, 10% PEG-4000, Seeded, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.07 α = 90
b = 91.46 β = 90
c = 120.5 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2009-08-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE OTHER 1.541790 -- --

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
2.18 72.85 100.0 0.238 0.256 -- 7.2 46372 46372 0.0 -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)
2.18 2.3 100.0 0.011 -- 0.7 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 2.18 72.85 -- -- 46314 44019 2286 99.98 -- 0.19972 0.1968 0.25726 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 2.18 2.237 -- 170 3222 0.248 0.326 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.744
Anisotropic B[1][1] -0.78
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.83
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.78
r_scbond_it 2.317
r_mcangle_it 1.403
r_mcbond_it 0.745
r_gen_planes_refined 0.007
r_chiral_restr 0.094
r_dihedral_angle_4_deg 19.983
r_dihedral_angle_3_deg 14.116
r_dihedral_angle_2_deg 31.913
r_dihedral_angle_1_deg 5.739
r_angle_refined_deg 1.468
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5027
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 366

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.3.15 data processing