X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 20% PEG 3000, 0.1 M HEPES buffer, 0.2 M Sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.42 α = 90
b = 82.56 β = 90
c = 91.32 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 -- 2007-11-05
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97920 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
2.3 40 99.3 0.183 -- -- 11.5 21647 21647 0.0 0.0 48.3
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)
2.3 2.38 96.7 0.67 -- 1.95 6.5 2068

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 2.3 40.0 -- 0.0 21442 21442 1100 98.38 0.1702 0.1702 0.1685 0.2007 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 2.3 2.36 1430 71 1359 0.216 0.316 -- 90.22
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.982
Anisotropic B[1][1] 1.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.92
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.548
r_dihedral_angle_2_deg 29.772
r_gen_planes_refined 0.006
r_mcbond_it 0.856
r_dihedral_angle_1_deg 4.979
r_mcangle_it 1.29
r_symmetry_hbond_refined 0.298
r_scangle_it 4.069
r_chiral_restr 0.113
r_nbtor_refined 0.304
r_dihedral_angle_3_deg 16.48
r_nbd_refined 0.203
r_symmetry_vdw_refined 0.209
r_scbond_it 2.433
r_dihedral_angle_4_deg 21.62
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.168
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3011
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 155

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.004
SBC-Collect data collection
HKL-3000 data reduction
SHELXD phasing
MLPHARE phasing
DM phasing
SOLVE phasing
RESOLVE phasing
HKL-3000 phasing