X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4
Temperature 298.0
Details 25% PEG 1500, 0.1M MES, Malic acid, Tris, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.61 α = 90
b = 86.77 β = 90
c = 116.54 γ = 90
Symmetry
Space Group F 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2010-07-24
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.000 SSRL BL12-2

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
1.72 26.53 97.2 -- 0.06 -- 4.0 15756 15756 -- -- --
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)
1.72 1.81 98.8 0.502 0.502 1.2 4.1 2316

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 1.72 25.397 -- 0.0 -- 15169 1524 93.32 -- 0.173 0.169 0.2077 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 1.72 1.7755 -- 131 1142 0.2546 0.3106 -- 87.0
X Ray Diffraction 1.7755 1.839 -- 132 1179 0.2185 0.2303 -- 90.0
X Ray Diffraction 1.839 1.9126 -- 141 1201 0.2102 0.2769 -- 91.0
X Ray Diffraction 1.9126 1.9996 -- 128 1162 0.1957 0.2629 -- 89.0
X Ray Diffraction 1.9996 2.105 -- 136 1232 0.1684 0.224 -- 93.0
X Ray Diffraction 2.105 2.2368 -- 140 1274 0.1478 0.1994 -- 97.0
X Ray Diffraction 2.2368 2.4093 -- 146 1309 0.1539 0.1976 -- 98.0
X Ray Diffraction 2.4093 2.6516 -- 139 1280 0.1549 0.1997 -- 97.0
X Ray Diffraction 2.6516 3.0347 -- 137 1228 0.1543 0.1815 -- 91.0
X Ray Diffraction 3.0347 3.8213 -- 146 1311 0.1535 0.1813 -- 98.0
X Ray Diffraction 3.8213 25.3993 -- 148 1327 0.1774 0.2118 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.115
Anisotropic B[1][1] 3.9518
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.2148
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.737
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.168
f_plane_restr 0.003
f_chiral_restr 0.048
f_angle_d 0.743
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1124
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 109

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALA version: 3.3.16 data reduction