X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details 3.5M Na formate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 147.82 α = 90
b = 147.82 β = 90
c = 117.69 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Mirrors 2007-10-24
Diffraction Radiation
Monochromator Protocol
Si 111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97929 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 47.78 99.9 0.126 -- -- 13.9 58423 58423 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)
2.3 2.35 99.0 0.931 -- 2.5 10.6 3809

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 47.78 0.0 0.0 55302 55302 2943 99.74 0.17462 0.17462 0.17269 0.21123 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 4190 235 3955 0.236 0.285 -- 98.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.465
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.15
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.193
r_dihedral_angle_1_deg 6.078
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 20.468
r_dihedral_angle_3_deg 16.025
r_mcangle_it 1.221
r_angle_refined_deg 1.407
r_xyhbond_nbd_refined 0.137
r_symmetry_vdw_refined 0.183
r_bond_refined_d 0.013
r_chiral_restr 0.095
r_nbtor_refined 0.299
r_symmetry_hbond_refined 0.217
r_dihedral_angle_2_deg 38.579
r_scangle_it 3.289
r_mcbond_it 0.711
r_scbond_it 2.05
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5616
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 450

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
SBC-Collect data collection
HKL-3000 data reduction
HKL-3000 data scaling
SHELXD phasing
MLPHARE phasing
DM phasing
RESOLVE phasing
HKL-3000 phasing