X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING DROP, temperature 295K; Cryo: oil, paratone

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 279.62 α = 90
b = 45.58 β = 101.58
c = 112.33 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 225 mm CCD Beryllium lenses 2009-09-13
Diffraction Radiation
Monochromator Protocol
Diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.14 30 98.2 0.084 -- -- 6.6 75710 75710 -- -3.0 34.7
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)
2.14 2.18 93.5 0.491 -- 3.5 6.0 3610

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 2.14 29.93 -- -- 71864 71864 3806 98.0 0.21387 0.21387 0.21092 0.26879 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 2.14 2.199 4985 232 4985 0.297 0.323 -- 92.53
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Individual Isotropic
Mean Isotropic B 27.209
Anisotropic B[1][1] -1.57
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.23
Anisotropic B[2][2] 5.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.47
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.013
r_dihedral_angle_4_deg 10.682
r_scbond_it 3.469
r_bond_other_d 0.001
r_dihedral_angle_2_deg 30.664
r_chiral_restr 0.087
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_dihedral_angle_3_deg 11.693
r_mcbond_it 1.286
r_angle_refined_deg 1.453
r_dihedral_angle_1_deg 2.762
r_angle_other_deg 0.87
r_mcangle_it 2.147
r_scangle_it 4.87
r_mcbond_other 0.375
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9900
Nucleic Acid Atoms 0
Heterogen Atoms 243
Solvent Atoms 555

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
PHENIX model building
REFMAC refinement version: 5.5.0102
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing