X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Details 0.1 M HEPES sodium pH 7.5, 1.4 M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 110K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.93 α = 90
b = 103.1 β = 90
c = 33.87 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2009-10-14
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A

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
2.45 103.1 99.8 0.133 -- -- 13.3 11560 11538 0.0 0.0 28.9
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)
2.45 2.58 99.9 0.313 -- 9.4 13.5 1652

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 2.45 65.552 -- 0.04 11379 11379 540 98.68 -- 0.2198 0.2173 0.2668 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 2.45 2.6965 -- 131 2601 0.2158 0.3016 -- 98.0
X Ray Diffraction 2.6965 3.0867 -- 141 2671 0.2183 0.26 -- 99.0
X Ray Diffraction 3.0867 3.8889 -- 143 2702 0.1949 0.2809 -- 99.0
X Ray Diffraction 3.8889 65.575 -- 125 2865 0.2202 0.2345 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 17.54
Anisotropic B[1][1] 6.996
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.7672
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.2288
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.095
f_plane_restr 0.005
f_angle_d 1.498
f_dihedral_angle_d 19.176
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2118
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 126

Software

Software
Software Name Purpose
CBASS data collection
PHASER phasing
PHENIX refinement version: (phenix.refine)
MOSFLM data reduction
SCALA data scaling