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_scbond_it 2.882
r_mcangle_it 1.529
r_mcbond_it 0.796
r_gen_planes_refined 0.007
r_chiral_restr 0.116
r_dihedral_angle_4_deg 13.748
r_dihedral_angle_3_deg 12.645
r_dihedral_angle_2_deg 35.619
r_dihedral_angle_1_deg 6.148
r_angle_refined_deg 1.592
r_bond_refined_d 0.016
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
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALEPACK data reduction
DENZO data collection