X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 100mM Tris pH 7.0, 20% PEG 2000 mono-methyl-ether, 3% PEG 3350, 30mM NaF, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.6 α = 90
b = 79.66 β = 90.02
c = 124.54 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
CCD MARRESEARCH -- 2007-07-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.00680 SLS X06SA

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
2.2 41.52 99.5 0.106 -- -- 4.11 41194 41211 -- -- 35.8
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)
2.2 2.3 99.3 0.273 -- 4.54 4.11 5113

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 2.2 41.52 -- 0.0 -- 39149 2061 100.0 -- 0.1713 0.16846 0.22518 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 2.2 2.257 -- 149 2821 0.185 0.276 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.053
Anisotropic B[1][1] 0.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.08
Anisotropic B[2][2] 0.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.92
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 3.201
r_chiral_restr 0.116
r_mcangle_it 1.755
r_angle_refined_deg 1.855
r_gen_planes_refined 0.008
r_bond_refined_d 0.02
r_dihedral_angle_4_deg 18.071
r_mcbond_it 0.934
r_scangle_it 5.066
r_dihedral_angle_1_deg 6.304
r_dihedral_angle_3_deg 15.626
r_dihedral_angle_2_deg 36.661
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6178
Nucleic Acid Atoms 237
Heterogen Atoms 88
Solvent Atoms 300

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0063
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
XSCALE data scaling
PHASER phasing