X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 289.0
Details 2.4 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.38 α = 90
b = 82.38 β = 90
c = 74.34 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 -- 2007-10-04
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97857 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
2.15 50 99.9 0.059 -- -- 11.6 14481 14459 -- -3.0 39.7
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)
2.15 2.23 100.0 0.416 -- 7.11 11.9 1411

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 2.15 41.2 -- 0.0 14417 14417 726 99.83 0.1921 0.1921 0.19093 0.21447 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 2.15 2.206 -- 56 985 0.178 0.221 -- 99.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.329
Anisotropic B[1][1] 0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.4
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.514
r_nbtor_refined 0.298
r_scangle_it 3.429
r_mcbond_it 0.86
r_symmetry_hbond_refined 0.282
r_nbd_refined 0.195
r_angle_refined_deg 1.256
r_chiral_restr 0.085
r_mcangle_it 1.249
r_dihedral_angle_3_deg 12.874
r_dihedral_angle_2_deg 39.529
r_xyhbond_nbd_refined 0.145
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 6.879
r_dihedral_angle_1_deg 4.589
r_bond_refined_d 0.015
r_symmetry_vdw_refined 0.257
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1447
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 103

Software

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