X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 291.0
Details pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.95 α = 90
b = 71.08 β = 106.66
c = 75.52 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++ -- 2010-07-01
Diffraction Radiation
Monochromator Protocol
Cu Kalpha anode SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.54178 -- --

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 50 98.0 -- -- -- -- -- 33190 2.0 2.0 24.2
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 86.4 0.354 0.354 3.073 3.5 5211

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 2.0 24.491 -- 0.13 -- 31225 1570 92.75 0.1871 0.1871 0.1852 0.2222 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 1.9998 2.0643 -- 110 2119 0.2227 0.2769 -- 73.0
X Ray Diffraction 2.0643 2.1381 -- 120 2426 0.2237 0.2831 -- 84.0
X Ray Diffraction 2.1381 2.2236 -- 138 2613 0.2056 0.2781 -- 90.0
X Ray Diffraction 2.2236 2.3247 -- 129 2654 0.1912 0.2326 -- 92.0
X Ray Diffraction 2.3247 2.4472 -- 146 2756 0.1985 0.2203 -- 94.0
X Ray Diffraction 2.4472 2.6004 -- 139 2740 0.1972 0.2362 -- 95.0
X Ray Diffraction 2.6004 2.8009 -- 150 2803 0.1995 0.2613 -- 97.0
X Ray Diffraction 2.8009 3.0822 -- 160 2835 0.1919 0.2373 -- 98.0
X Ray Diffraction 3.0822 3.5271 -- 154 2882 0.1786 0.2317 -- 99.0
X Ray Diffraction 3.5271 4.4395 -- 160 2906 0.1547 0.1701 -- 100.0
X Ray Diffraction 4.4395 24.4929 -- 164 2921 0.1569 0.184 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.7043
Anisotropic B[1][1] 16.2289
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.8527
Anisotropic B[2][2] -9.9994
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.2296
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.045
f_bond_d 0.01
f_dihedral_angle_d 19.273
f_chiral_restr 0.106
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3136
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 380

Software

Software
Software Name Purpose
DDT data collection
PHASES phasing
PHENIX refinement version: (phenix.refine: 1.5_2)
HKL-2000 data reduction
HKL-2000 data scaling