X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details 1 uL 20 mg/mL protein in 25 mM sodium acetate pH 5.0 + 1 uL precipitate solution (1.8 M ammonium sulfate), VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.67 α = 90
b = 113.5 β = 108.75
c = 79.91 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2011-04-14
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.9815 KURCHATOV SNC K4.4

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
1.67 75.67 96.3 0.038 0.038 -- 2.8 69231 65537 0.0 0.0 29.6
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)
1.67 1.77 90.6 0.434 0.434 2.13 2.5 9802

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 1.67 75.67 -- 0.0 65537 62208 3329 97.01 -- 0.16628 0.16493 0.19116 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 1.674 1.717 -- 229 4238 0.28 0.29 -- 90.02
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.462
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.35
Anisotropic B[2][2] 1.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.87
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 8.762
r_scangle_it 3.624
r_scbond_it 2.551
r_mcangle_it 1.682
r_mcbond_other 0.352
r_mcbond_it 1.085
r_gen_planes_other 0.001
r_gen_planes_refined 0.009
r_chiral_restr 0.113
r_dihedral_angle_4_deg 15.948
r_dihedral_angle_3_deg 12.497
r_dihedral_angle_2_deg 34.411
r_dihedral_angle_1_deg 7.229
r_angle_other_deg 1.422
r_angle_refined_deg 1.912
r_bond_other_d 0.001
r_bond_refined_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4181
Nucleic Acid Atoms 0
Heterogen Atoms 200
Solvent Atoms 445

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0072 refinement
MOLREP model building
HKL-2000 data collection