X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 289.0
Details 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.0, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.18 α = 90
b = 76.91 β = 90
c = 294.96 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-11-07
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U

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
2.34 147.48 95.7 0.057 -- -- 6.4 -- 37249 5.0 -- --
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)
2.34 2.38 76.0 0.105 -- -- 4.1 1407

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
SAD 2.34 47.414 -- -- -- 33809 1781 95.66 -- 0.21696 0.21445 0.26363 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 2.34 2.398 -- 99 1960 0.249 0.313 -- 76.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.122
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.21
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.807
r_scbond_it 1.078
r_mcangle_it 0.833
r_mcbond_it 0.446
r_gen_planes_refined 0.004
r_chiral_restr 0.07
r_dihedral_angle_4_deg 13.906
r_dihedral_angle_3_deg 15.739
r_dihedral_angle_2_deg 31.746
r_dihedral_angle_1_deg 4.865
r_angle_refined_deg 1.095
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5182
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 270

Software

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