X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 292.0
Details Tris-HCl, NaCl, ethylene glycol, PEG 6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.02 α = 90
b = 108.78 β = 90
c = 109.56 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 4 -- 2001-09-17
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1

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
1.9 55.05 99.6 0.114 -- -- 11.4 63850 63452 0.0 4.3 15.0
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)
1.9 1.95 95.1 0.264 -- 4.3 9.0 --

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 1.9 76.7 -- 0.0 60342 60342 3210 99.53 0.13699 0.13699 0.13498 0.17459 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 1.9 1.95 4411 209 -- 0.145 0.206 -- 95.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic temperature factors
Mean Isotropic B 8.67
Anisotropic B[1][1] -0.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.95
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.199
r_nbd_refined 0.234
r_gen_planes_other 0.002
r_gen_planes_refined 0.008
r_chiral_restr 0.114
r_dihedral_angle_3_deg 16.412
r_dihedral_angle_1_deg 4.507
r_angle_other_deg 0.827
r_angle_refined_deg 1.743
r_bond_other_d 0.001
r_bond_refined_d 0.021
r_xyhbond_nbd_refined 0.224
r_xyhbond_nbd_other 0.149
r_symmetry_vdw_refined 0.552
r_symmetry_vdw_other 0.303
r_symmetry_hbond_refined 0.48
r_mcbond_it 0.972
r_mcangle_it 1.734
r_scbond_it 3.095
r_scangle_it 4.938
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.127
Luzzati ESD (R-Free Set) 0.118
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6381
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 847

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHAKE-N-BAKE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
SnB model building