X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 120mM Tris-HCl, 11% PEG 4000, 200mM MgCl2, 90mM NiCl2, 50mM Na2S2O3, 50mM L-serine, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 167.03 α = 90
b = 167.03 β = 90
c = 211.11 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2007-12-03
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00000 SPRING-8 BL41XU

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
3.89 50 94.1 0.103 0.103 -- 9.1 28051 26396 -- -2.0 130.32
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)
3.9 4.04 86.8 0.736 0.736 2.02 8.1 2717

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 3.893 49.247 -- 1.35 28003 26354 1345 94.11 -- 0.2235 0.2203 0.2822 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 3.8931 4.0322 -- 118 2244 0.3686 0.4 -- 87.0
X Ray Diffraction 4.0322 4.1935 -- 113 2340 0.3127 0.3535 -- 89.0
X Ray Diffraction 4.1935 4.3843 -- 120 2400 0.2728 0.2989 -- 91.0
X Ray Diffraction 4.3843 4.6152 -- 149 2388 0.2183 0.2916 -- 92.0
X Ray Diffraction 4.6152 4.9042 -- 138 2485 0.1957 0.2515 -- 95.0
X Ray Diffraction 4.9042 5.2824 -- 143 2544 0.1932 0.287 -- 96.0
X Ray Diffraction 5.2824 5.8132 -- 134 2583 0.2289 0.2681 -- 98.0
X Ray Diffraction 5.8132 6.6527 -- 152 2607 0.2501 0.3266 -- 98.0
X Ray Diffraction 6.6527 8.375 -- 133 2668 0.197 0.2661 -- 98.0
X Ray Diffraction 8.375 49.2505 -- 145 2750 0.1879 0.2515 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 209.76
Anisotropic B[1][1] -46.8339
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -46.8339
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 93.6677
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.55
f_plane_restr 0.004
f_chiral_restr 0.07
f_angle_d 1.222
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16913
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement