X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.3
Temperature 295.0
Details Crystallization: The JCSG+ Suite (D12): 0.04 M Potasium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol Protein: 8.7 mg/ml in 10 mM Tris-HCl pH 8.3, 0.25 M NaCl, 5 mM BME Freezing: crystallization condition

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.61 α = 90
b = 96.34 β = 98.22
c = 129.62 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2014-08-14
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 39 100.0 0.052 -- -- 3.8 -- 115793 -- -- --
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)
2.0 2.07 100.0 0.55 -- 2.5 3.8 --

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 2.0 38.79 -- -- -- 101473 5263 92.0 -- 0.169 0.168 0.199 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 2.0 2.05 -- 270 5024 0.207 0.237 -- 62.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.0
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.29
Anisotropic B[2][2] 0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.57
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.008
r_angle_other_deg 1.123
r_bond_other_d 0.005
r_dihedral_angle_4_deg 13.661
r_dihedral_angle_1_deg 3.459
r_angle_refined_deg 1.362
r_chiral_restr 0.082
r_dihedral_angle_2_deg 31.966
r_gen_planes_other 0.005
r_dihedral_angle_3_deg 11.978
r_gen_planes_refined 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11136
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 1312

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0029
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing