X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details Drops of 10 uL (0.3 mM protein; 100 mM small imidazole; 0.8 M sodium citrate; 50 mM Tris-HCl; pH 8.0) were equilibrated against the precipitant solution (1.6 M sodium citrate; 50 mM Tris-HCl; pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.29 α = 90
b = 41.19 β = 104.44
c = 71.94 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++ -- 2011-07-10
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
1.7 19.96 -- -- -- -- -- -- 26325 -- -- --

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 1.6984 19.959 -- 0.0 26711 25878 1298 96.88 -- 0.1674 0.1654 0.2056 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 1.6984 1.7664 -- 136 2503 0.2063 0.2429 -- 90.0
X Ray Diffraction 1.7664 1.8467 -- 127 2651 0.1784 0.264 -- 94.0
X Ray Diffraction 1.8467 1.944 -- 133 2658 0.1542 0.216 -- 96.0
X Ray Diffraction 1.944 2.0657 -- 154 2702 0.1579 0.2447 -- 97.0
X Ray Diffraction 2.0657 2.225 -- 145 2758 0.1591 0.209 -- 98.0
X Ray Diffraction 2.225 2.4485 -- 149 2761 0.1606 0.2123 -- 99.0
X Ray Diffraction 2.4485 2.802 -- 150 2805 0.1745 0.2162 -- 99.0
X Ray Diffraction 2.802 3.5271 -- 151 2835 0.1791 0.2087 -- 100.0
X Ray Diffraction 3.5271 19.9609 -- 153 2907 0.1525 0.1684 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.7754
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.2177
Anisotropic B[2][2] -1.583
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.3584
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.109
f_dihedral_angle_d 13.165
f_bond_d 0.015
f_angle_d 1.544
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2044
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 144

Software

Software
Software Name Purpose
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.11
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing