X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 273.0
Details 1.0 ul protein 11 mg/ml 0.4 ul crystallization buffer, 8% PEG8000, 40% PEG 400, 0.04M Hepes, 3.5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.31 α = 90
b = 54.11 β = 90
c = 94.38 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 -- 2005-10-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.9794 ALS 8.2.2

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
1.15 50 96.2 0.098 -- -- 3.0 -- 69478 -- -- --
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)
1.15 1.19 84.6 0.233 -- -- 2.0 6040

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 1.3 20.0 -- 0.0 -- 44581 2269 88.43 0.161 -- 0.161 0.18 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 1.3 1.334 3142 159 2983 0.176 0.189 -- 86.25
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 7.04
Anisotropic B[1][1] 0.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.09
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.725
r_bond_other_d 0.0
r_dihedral_angle_4_deg 20.367
r_bond_refined_d 0.013
r_nbtor_refined 0.184
r_dihedral_angle_2_deg 35.83
r_dihedral_angle_3_deg 13.881
r_nbtor_other 0.093
r_nbd_other 0.242
r_mcbond_other 0.665
r_symmetry_vdw_refined 0.433
r_dihedral_angle_1_deg 8.286
r_xyhbond_nbd_refined 0.188
r_symmetry_vdw_other 0.348
r_scangle_it 5.881
r_nbd_refined 0.267
r_scbond_it 4.621
r_gen_planes_refined 0.006
r_mcangle_it 3.006
r_gen_planes_other 0.002
r_angle_refined_deg 1.462
r_chiral_restr 0.108
r_symmetry_hbond_refined 0.204
r_mcbond_it 2.797
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1531
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 282

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.10
RESOLVE phasing version: 2.10
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000