X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details Reservoir: 16% PEG3350, 0.1M MES pH 6.5, 0.1M MgCl2, 0.1M 6-aminohexanoic acid. Protein: 26.2mg/ml. Drops: 1+1 microliter, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.6 α = 90
b = 83.8 β = 90
c = 116.72 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 -- 2006-06-11
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal, Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97900 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
1.65 50 97.1 0.087 -- -- 5.3 -- 62805 0.0 0.0 23.0
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)
1.65 1.66 99.2 0.627 -- 3.6 4.6 --

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 1.65 34.04 0.0 0.0 -- 57112 3089 95.96 -- 0.19792 0.19575 0.23871 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 1.65 1.694 4185 232 4185 0.231 0.29 -- 96.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.54
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.4
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.191
r_symmetry_hbond_refined 0.177
r_dihedral_angle_4_deg 15.991
r_bond_refined_d 0.016
r_scangle_it 3.335
r_gen_planes_refined 0.006
r_nbtor_refined 0.303
r_dihedral_angle_3_deg 13.711
r_mcbond_it 0.877
r_scbond_it 2.214
r_angle_refined_deg 1.479
r_dihedral_angle_1_deg 5.389
r_chiral_restr 0.105
r_xyhbond_nbd_refined 0.164
r_dihedral_angle_2_deg 34.903
r_mcangle_it 1.257
r_nbd_refined 0.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3882
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 472

Software

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