X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.0
Details Protein: 1.5mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 0.2M Calcium acetate, 0.1M Na Cacodylate pH 6.0, 18% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.61 α = 90
b = 85.8 β = 122.39
c = 77.95 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 MARMOSAIC 300 mm CCD Beryllium lenses 2009-07-31
Diffraction Radiation
Monochromator Protocol
Diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G

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
2.4 30 100.0 0.069 -- -- 8.1 26058 26058 -- -3.0 55.0
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)
2.4 2.44 100.0 0.577 -- 4.1 7.8 1337

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 2.4 29.16 -- -- 24593 24593 1317 99.92 0.17973 0.17973 0.17693 0.23229 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 2.4 2.462 1822 92 1822 0.229 0.307 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Thermal Factors Individually Isotropically Refined
Mean Isotropic B 63.502
Anisotropic B[1][1] -0.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.67
Anisotropic B[2][2] -1.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.66
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.016
r_scbond_other 3.51
r_mcbond_it 3.164
r_bond_other_d 0.001
r_dihedral_angle_3_deg 10.787
r_long_range_B_other 8.427
r_dihedral_angle_1_deg 2.675
r_angle_refined_deg 1.403
r_bond_refined_d 0.009
r_dihedral_angle_4_deg 10.228
r_scbond_it 3.51
r_long_range_B_refined 8.453
r_mcbond_other 3.164
r_mcangle_other 5.018
r_chiral_restr 0.082
r_scangle_other 5.561
r_mcangle_it 5.019
r_dihedral_angle_2_deg 25.561
r_angle_other_deg 0.7
r_gen_planes_refined 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5088
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 138

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
PHENIX model building
REFMAC refinement version: 5.8.0046
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing