X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 18-20% PEG6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.23 α = 90
b = 67.14 β = 90
c = 96.83 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 2M -- 2015-05-07
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2

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
1.45 16.77 99.15 0.08072 -- -- 4.4 228593 51455 -- -- 19.46
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)
1.45 1.502 98.97 0.7014 -- 1.8 4.7 --

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 1.45 16.77 -- 1.34 -- 51350 2504 98.95 -- 0.1532 0.1516 0.1852 HKL reflections copied from pdb entry 2wph
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 1.45 1.4779 -- 125 2705 0.2868 0.3171 -- 98.0
X Ray Diffraction 1.4779 1.508 -- 118 2641 0.2649 0.2632 -- 98.0
X Ray Diffraction 1.508 1.5408 -- 135 2655 0.2473 0.2716 -- 98.0
X Ray Diffraction 1.5408 1.5766 -- 151 2628 0.2142 0.2617 -- 97.0
X Ray Diffraction 1.5766 1.616 -- 146 2654 0.2056 0.2348 -- 98.0
X Ray Diffraction 1.616 1.6597 -- 118 2662 0.1939 0.2045 -- 98.0
X Ray Diffraction 1.6597 1.7085 -- 145 2705 0.1824 0.2432 -- 99.0
X Ray Diffraction 1.7085 1.7635 -- 122 2667 0.1739 0.2179 -- 99.0
X Ray Diffraction 1.7635 1.8265 -- 126 2729 0.168 0.2229 -- 99.0
X Ray Diffraction 1.8265 1.8995 -- 148 2691 0.1691 0.1996 -- 100.0
X Ray Diffraction 1.8995 1.9859 -- 124 2748 0.1589 0.1832 -- 100.0
X Ray Diffraction 1.9859 2.0904 -- 155 2717 0.1482 0.1806 -- 100.0
X Ray Diffraction 2.0904 2.2211 -- 141 2747 0.1476 0.1618 -- 100.0
X Ray Diffraction 2.2211 2.3921 -- 152 2691 0.144 0.1739 -- 99.0
X Ray Diffraction 2.3921 2.632 -- 155 2727 0.147 0.1786 -- 99.0
X Ray Diffraction 2.632 3.011 -- 145 2743 0.1506 0.1716 -- 99.0
X Ray Diffraction 3.011 3.7863 -- 156 2787 0.1347 0.1927 -- 100.0
X Ray Diffraction 3.7863 16.7759 -- 142 2949 0.1258 0.1547 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.3
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.092
f_plane_restr 0.009
f_bond_d 0.014
f_dihedral_angle_d 14.992
f_angle_d 1.546
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2225
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 256

Software

Software
Software Name Purpose
iMOSFLM data reduction version: 7.1.1
Aimless data scaling version: 0.3.11
MOLREP phasing version: 11.2.08
REFMAC refinement version: 5.8.0073
Coot model building version: 0.8.1-pre
PHENIX refinement version: 1.9-1692
PDB_EXTRACT data extraction version: 3.15