X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details 0.1M Tris-HCl, 0.2M MgCl2, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.34 α = 90
b = 100.62 β = 90
c = 134.31 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2006-04-19
Diffraction Radiation
Monochromator Protocol
Si 111 channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9798 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 67.12 97.54 0.122 -- -- 8.7 27040 26375 -- 2.0 22.0
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)
2.0 2.05 83.28 0.62 -- 2.0 6.5 2087

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 2.0 67.12 0.0 0.0 26375 26375 1402 97.54 0.1897 0.1897 0.18737 0.23484 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 2.0 2.052 1738 103 1635 0.225 0.309 -- 83.28
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.917
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.652
r_gen_planes_refined 0.005
r_mcangle_it 1.413
r_nbd_refined 0.22
r_symmetry_hbond_refined 0.17
r_chiral_restr 0.08
r_mcbond_it 1.255
r_nbtor_refined 0.179
r_mcbond_other 0.205
r_bond_other_d 0.001
r_scbond_it 2.107
r_dihedral_angle_4_deg 16.744
r_gen_planes_other 0.001
r_nbd_other 0.195
r_scangle_it 3.018
r_angle_other_deg 0.945
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.16
r_symmetry_vdw_refined 0.183
r_angle_refined_deg 1.419
r_dihedral_angle_2_deg 35.466
r_dihedral_angle_3_deg 15.092
r_nbtor_other 0.088
r_symmetry_vdw_other 0.324
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.035
Luzzati Sigma A (Observed) 0.34
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.04
Luzzati Sigma A (R-Free Set) 0.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2466
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 223

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
SBC-Collect data collection
HKL-2000 data reduction
HKL-2000 data scaling