X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.0
Details 1.2 M NaCitrate and 0.1 M Tris, pH 8.5, vapor diffusion hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.05 α = 90
b = 51.39 β = 90
c = 69.26 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 315r -- 2012-07-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178 -- --

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
1.8 50 95.8 0.03 -- -- 7.6 13540 13540 0.0 0.0 23.5
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)
1.8 1.83 93.7 0.345 -- -- 6.8 651

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 29.12 -- 0.0 -- 13452 664 95.49 0.19016 0.1902 0.1875 0.2429 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 1.802 1.848 -- 53 879 0.296 0.36 -- 92.46
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.3598
Anisotropic B[1][1] -1.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.173
r_mcangle_it 2.916
r_mcbond_it 1.813
r_gen_planes_refined 0.007
r_chiral_restr 0.104
r_dihedral_angle_4_deg 4.982
r_dihedral_angle_3_deg 14.187
r_dihedral_angle_2_deg 38.17
r_dihedral_angle_1_deg 6.558
r_angle_refined_deg 1.359
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1185
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 99

Software

Computing
Computing Package Purpose
Jdirector Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
MOLREP 11.0 Structure Solution
REFMAC 5.7.0032, COOT 0.6.2 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction