X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.4
Temperature 294.0
Details 20% PEG 3350, 0.2 M Magnesium nitrate, 0.3 M NSDB-256, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.34 α = 90
b = 44.75 β = 108.62
c = 32.66 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-10-27
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM

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
1.88 26.3 99.5 0.067 -- -- 10.4 8519 8519 0.0 0.0 36.4
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)
1.88 1.94 100.0 0.445 -- 6.2 10.5 492

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
SAD 1.88 26.27 0.0 0.0 8456 8456 407 98.43 0.19 0.19 0.188 0.222 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 1.88 1.929 677 29 548 0.296 0.363 -- 91.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.636
Anisotropic B[1][1] 0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.28
Anisotropic B[2][2] 0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.67
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_mcangle_it 1.706
r_dihedral_angle_3_deg 17.176
r_dihedral_angle_1_deg 6.518
r_gen_planes_refined 0.006
r_mcbond_other 0.216
r_chiral_restr 0.091
r_scangle_it 4.373
r_angle_other_deg 0.914
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 33.327
r_scbond_it 2.614
r_bond_refined_d 0.017
r_dihedral_angle_4_deg 16.598
r_mcbond_it 0.922
r_angle_refined_deg 1.488
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 798
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 88

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.5.0054
PDB_EXTRACT data extraction version: 3.006
SBC-Collect data collection
HKL-3000 data reduction
SHELXD phasing
MLPHARE phasing
DM phasing
SOLVE phasing
RESOLVE phasing
HKL-3000 phasing