X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 289.0
Details 0.2 M calcium acetate, 0.1 M MES buffer, 20% PEG 8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.5 α = 90
b = 107.91 β = 90
c = 252.85 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 -- 2010-07-12
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
1.96 45.9 97.8 0.082 -- -- 5.1 113973 113973 0.0 0.0 --
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)
1.96 1.99 89.5 0.501 -- 2.24 3.5 --

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 1.97 45.9 -- -- 113552 107866 5686 97.26 -- 0.19816 0.1956 0.2466 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 1.966 2.017 -- 382 7056 0.274 0.326 -- 87.65
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.669
Anisotropic B[1][1] 0.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.74
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.018
r_dihedral_angle_1_deg 6.441
r_mcbond_it 0.868
r_scbond_it 2.48
r_dihedral_angle_4_deg 20.075
r_chiral_restr 0.095
r_dihedral_angle_2_deg 36.176
r_gen_planes_other 0.001
r_angle_other_deg 0.941
r_mcangle_it 1.485
r_bond_other_d 0.001
r_angle_refined_deg 1.618
r_gen_planes_refined 0.007
r_mcbond_other 0.256
r_dihedral_angle_3_deg 16.599
r_scangle_it 3.951
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10914
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 653

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