X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 289.0
Details JCSG condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350, 26.9 mg/mL protein, Crystal Tracking ID 202955h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.3 α = 108.5
b = 68.08 β = 107.11
c = 73.54 γ = 104.95
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2009-07-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
2.15 50 95.6 0.056 -- -- 4.0 -- 48256 -- -- --
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)
2.15 2.23 90.8 0.178 -- 7.4 3.8 4584

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 2.15 33.9 -- 0.0 -- 48228 2412 95.43 -- 0.184 0.182 0.223 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 2.15 2.206 -- 182 3174 0.2 0.269 -- 88.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.629
Anisotropic B[1][1] 0.61
Anisotropic B[1][2] 1.06
Anisotropic B[1][3] -0.39
Anisotropic B[2][2] 0.41
Anisotropic B[2][3] 0.05
Anisotropic B[3][3] -0.67
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.268
r_gen_planes_refined 0.006
r_scangle_it 2.749
r_bond_refined_d 0.011
r_dihedral_angle_2_deg 36.008
r_dihedral_angle_3_deg 15.203
r_dihedral_angle_4_deg 16.51
r_scbond_it 1.615
r_mcbond_it 0.502
r_mcangle_it 0.943
r_chiral_restr 0.084
r_dihedral_angle_1_deg 5.979
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7208
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 496

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data reduction
HKL-2000 data scaling