X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 18% PEG-3350, 0.22M potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.45 α = 90
b = 93.1 β = 90
c = 94.37 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2010-07-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 1.0000 ALS 5.0.1

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
2.07 50 99.7 0.103 -- -- 5.8 -- 49114 -- -- --
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)
2.07 2.11 95.3 0.34 -- -- 5.2 2311

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 2.07 45.23 -- 0.0 -- 48971 2485 99.25 -- 0.1696 0.1678 0.2026 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 2.069 2.123 -- 178 3201 0.176 0.208 -- 94.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.2672
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.12
r_scbond_it 2.021
r_mcangle_it 1.33
r_mcbond_other 0.17
r_bond_refined_d 0.009
r_bond_other_d 0.001
r_angle_refined_deg 1.166
r_angle_other_deg 0.805
r_dihedral_angle_1_deg 5.906
r_dihedral_angle_2_deg 33.898
r_dihedral_angle_3_deg 12.588
r_dihedral_angle_4_deg 20.392
r_chiral_restr 0.072
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_mcbond_it 0.718
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5372
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 343

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
HKL data processing