X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.6M-1.7M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.29 α = 90
b = 61.78 β = 112.9
c = 70.52 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2009-06-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.54179 -- --

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 50 96.4 0.041 -- -- 4.0 -- 53546 -- -- --
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 1.81 92.7 0.248 -- -- 3.4 5095

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 1.75 64.97 -- 0.0 -- 50805 2715 96.39 0.161 0.162 0.161 0.186 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 1.75 1.795 -- 201 3570 0.282 0.338 -- 92.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.8707
Anisotropic B[1][1] 0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.75
Anisotropic B[2][2] -0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.93
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.856
r_dihedral_angle_3_deg 12.645
r_dihedral_angle_4_deg 13.748
r_scbond_it 2.882
r_bond_refined_d 0.016
r_dihedral_angle_2_deg 35.619
r_gen_planes_refined 0.007
r_chiral_restr 0.116
r_mcangle_it 1.529
r_mcbond_it 0.796
r_dihedral_angle_1_deg 6.148
r_angle_refined_deg 1.592
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3916
Nucleic Acid Atoms 0
Heterogen Atoms 102
Solvent Atoms 300

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC5 refinement
SCALEPACK data reduction
MOLREP molecular replacement
DENZO data collection
pdb_extract version: 3.11 data extraction