X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 30% PEG4000, 0.1 M Tris, 0.2 M lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.54 α = 90
b = 74.28 β = 90
c = 144.47 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 -- 2005-10-21
Diffraction Radiation
Monochromator Protocol
double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 1.00 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
2.49 90 100.0 0.112 -- -- 7.9 15987 15987 -- -3.0 41.7
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)
2.49 2.59 99.9 0.419 -- -- 7.6 1727

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 2.5 72.17 -- 0.0 15767 15767 800 99.98 0.177 0.177 0.175 0.223 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 2.5 2.565 1129 64 1065 0.198 0.314 -- 99.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.725
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.33
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.175
r_dihedral_angle_1_deg 3.797
r_chiral_restr 0.074
r_metal_ion_refined 0.173
r_symmetry_hbond_refined 0.124
r_nbtor_other 0.085
r_gen_planes_other 0.001
r_angle_other_deg 0.885
r_dihedral_angle_2_deg 30.193
r_dihedral_angle_3_deg 13.227
r_scangle_it 2.432
r_scbond_it 1.616
r_gen_planes_refined 0.003
r_dihedral_angle_4_deg 16.68
r_mcbond_it 1.681
r_bond_refined_d 0.008
r_symmetry_vdw_other 0.28
r_bond_other_d 0.001
r_nbd_other 0.19
r_mcangle_it 2.504
r_symmetry_vdw_refined 0.157
r_mcbond_other 0.331
r_nbd_refined 0.2
r_angle_refined_deg 1.533
r_xyhbond_nbd_refined 0.143
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2817
Nucleic Acid Atoms 0
Heterogen Atoms 109
Solvent Atoms 69

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
BOS data collection