X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 298.0
Details 1.6M Na-Citrate and 50 mM Tris-Cl at pH 7.8 used as precipitant solution. DMSO was used to dissolve the inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.29 α = 90
b = 41.28 β = 104.13
c = 72.06 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
IMAGE PLATE RIGAKU RAXIS IV++ -- 2010-07-26
Diffraction Radiation
Monochromator Protocol
Varimax Optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.49 50 96.4 0.07 -- -- 5.4 39684 38255 -- -- --
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)
1.49 1.54 90.1 0.261 -- -- 5.1 3569

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 1.491 25.346 -- 1.36 -- 38255 1895 96.68 -- 0.1574 0.1564 0.1782 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 1.491 1.5281 -- 127 2442 0.3699 0.3572 -- 91.0
X Ray Diffraction 1.5281 1.5694 -- 132 2508 0.2778 0.2863 -- 93.0
X Ray Diffraction 1.5694 1.6156 -- 124 2488 0.2174 0.2794 -- 95.0
X Ray Diffraction 1.6156 1.6678 -- 145 2538 0.173 0.1786 -- 95.0
X Ray Diffraction 1.6678 1.7274 -- 130 2575 0.1417 0.1329 -- 95.0
X Ray Diffraction 1.7274 1.7965 -- 127 2570 0.1311 0.1674 -- 96.0
X Ray Diffraction 1.7965 1.8782 -- 131 2583 0.1271 0.1831 -- 97.0
X Ray Diffraction 1.8782 1.9772 -- 130 2617 0.1334 0.1427 -- 97.0
X Ray Diffraction 1.9772 2.101 -- 138 2608 0.1348 0.1538 -- 98.0
X Ray Diffraction 2.101 2.2632 -- 133 2636 0.1431 0.1957 -- 98.0
X Ray Diffraction 2.2632 2.4908 -- 142 2669 0.1394 0.1488 -- 99.0
X Ray Diffraction 2.4908 2.8507 -- 145 2682 0.1451 0.1719 -- 99.0
X Ray Diffraction 2.8507 3.59 -- 144 2701 0.1487 0.1718 -- 100.0
X Ray Diffraction 3.59 25.3498 -- 147 2778 0.1691 0.1839 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.899
Anisotropic B[1][1] -1.0026
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0378
Anisotropic B[2][2] -0.8785
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.8811
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.945
f_plane_restr 0.007
f_chiral_restr 0.092
f_angle_d 1.371
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 208

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
phenix Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
HKL data reduction