X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.2
Temperature 298.0
Details 0.2 M sodium acetate (pH 6.2), 20% PEG 3350, 15% glycerol and 1 mM concentration of the ligand., VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.73 α = 90
b = 54.35 β = 107.52
c = 66.81 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-06-06
Diffraction Radiation
Monochromator Protocol
Ni filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D -- APS 21-ID-D

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
1.52 33.08 94.9 -- -- -- -- 45773 43465 2.0 2.0 --
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)
1.522 1.562 97.64 -- -- -- -- --

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 1.522 30.082 -- 2.0 45773 43465 2308 99.73 0.221 0.1851 0.1831 0.2221 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 1.522 1.562 -- 164 3150 0.221 0.262 -- 97.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.037
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.2
Anisotropic B[2][2] -0.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.16
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 33.244
r_dihedral_angle_1_deg 5.089
r_bond_refined_d 0.015
r_gen_planes_refined 0.008
r_scbond_it 3.181
r_chiral_restr 0.113
r_mcbond_it 1.078
r_dihedral_angle_4_deg 18.723
r_dihedral_angle_3_deg 13.173
r_mcangle_it 2.03
r_scangle_it 5.265
r_angle_refined_deg 1.654
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2123
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 394

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0072
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
DENZO data reduction
SCALEPACK data scaling
HKL-2000 data scaling
PHASER phasing