X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details 0.2 M tri-ammonium citrate, 20% PEG-3350, 10 mM glycine, 10 mM pyridoxal 5'-phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.08 α = 90
b = 86.53 β = 90
c = 301.81 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-10-10
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID

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
1.92 50 98.0 0.085 -- -- 6.1 136110 136110 0.0 0.0 38.1
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)
1.92 1.95 95.4 0.807 -- 2.02 6.1 6446

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 1.92 47.7 0.0 0.0 135637 135637 6799 97.75 0.1677 0.1677 0.1655 0.2076 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 1.92 1.971 9619 491 9128 0.262 0.278 -- 95.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.106
Anisotropic B[1][1] 2.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.71
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.517
r_bond_refined_d 0.017
r_scbond_it 2.555
r_chiral_restr 0.102
r_mcbond_it 0.862
r_mcbond_other 0.25
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_angle_refined_deg 1.598
r_dihedral_angle_1_deg 5.743
r_dihedral_angle_4_deg 16.81
r_dihedral_angle_2_deg 34.596
r_bond_other_d 0.001
r_angle_other_deg 0.964
r_dihedral_angle_3_deg 14.377
r_scangle_it 4.292
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12410
Nucleic Acid Atoms 0
Heterogen Atoms 127
Solvent Atoms 1057

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.5.0109
PDB_EXTRACT data extraction version: 3.10
SBC-Collect data collection
HKL-3000 data reduction
HKL-3000 data scaling
MOLREP phasing
HKL-3000 phasing