X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 0.1 M MOPS-NaOH, 75-150 mM MgSO4, 7-9% PEG8000, 5 mM beta-mercaptoethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 435.97 α = 90
b = 183 β = 108.99
c = 225.39 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 ADSC QUANTUM 315r -- 2008-10-10
-- -- -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- --
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A -- NSLS X6A
SYNCHROTRON NSLS BEAMLINE X25 -- NSLS X25
SYNCHROTRON CHESS BEAMLINE F1 -- CHESS F1

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
3.26 15 98.5 0.092 0.092 -- 2.5 252390 252390 1.0 1.0 79.38
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)
3.26 3.36 91.7 0.626 0.626 1.5 2.5 --

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 3.26 15.0 -- 1.33 -- 252275 2000 98.0 -- 0.243 0.243 0.265 --
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 3.26 3.3414 -- 120 15013 0.3855 0.4051 -- 83.0
X Ray Diffraction 3.3414 3.4307 -- 143 17989 0.3637 0.3402 -- 99.0
X Ray Diffraction 3.4307 3.5303 -- 145 18097 0.341 0.3763 -- 99.0
X Ray Diffraction 3.5303 3.6427 -- 145 18091 0.3247 0.3263 -- 100.0
X Ray Diffraction 3.6427 3.7709 -- 144 18063 0.3069 0.3246 -- 100.0
X Ray Diffraction 3.7709 3.9193 -- 144 18112 0.2826 0.3117 -- 100.0
X Ray Diffraction 3.9193 4.0942 -- 146 18158 0.2609 0.3059 -- 100.0
X Ray Diffraction 4.0942 4.3053 -- 145 18103 0.2359 0.272 -- 99.0
X Ray Diffraction 4.3053 4.5678 -- 145 18124 0.2061 0.2554 -- 100.0
X Ray Diffraction 4.5678 4.909 -- 144 18135 0.1968 0.2227 -- 99.0
X Ray Diffraction 4.909 5.3822 -- 145 18230 0.2223 0.2612 -- 100.0
X Ray Diffraction 5.3822 6.1144 -- 146 18127 0.2397 0.2597 -- 99.0
X Ray Diffraction 6.1144 7.5372 -- 144 18093 0.2236 0.2693 -- 99.0
X Ray Diffraction 7.5372 14.9999 -- 144 17940 0.1683 0.1577 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 118.36
Anisotropic B[1][1] -4.2964
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.4846
Anisotropic B[2][2] -5.4824
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.6016
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.821
f_dihedral_angle_d 22.888
f_bond_d 0.004
f_plane_restr 0.003
f_chiral_restr 0.058
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 98928
Nucleic Acid Atoms 0
Heterogen Atoms 581
Solvent Atoms 64

Software

Software
Software Name Purpose
PHENIX refinement version: 1.6.3_473
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing