X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 292.0
Details 12-16% PEG 8K, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.32 α = 90
b = 51.32 β = 90
c = 71.09 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2004-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9792 ESRF ID29

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 50 99.2 -- 0.065 -- 4.8 7656 7656 0.0 0.0 32.3
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 2.07 99.5 -- 0.33 3.36 2.8 1432

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
MIRAS 2.0 44.46 0.0 0.0 7336 7283 354 99.28 -- 0.22308 0.22149 0.25492 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 -- 30 528 0.306 0.332 -- 98.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.302
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] -0.29
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.88
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.187
r_mcbond_it 1.845
r_bond_refined_d 0.008
r_angle_refined_deg 1.363
r_xyhbond_nbd_refined 0.129
r_dihedral_angle_3_deg 17.194
r_mcangle_it 2.712
r_scbond_it 5.034
r_chiral_restr 0.094
r_dihedral_angle_1_deg 4.35
r_scangle_it 6.838
r_gen_planes_refined 0.004
r_symmetry_hbond_refined 0.174
r_symmetry_vdw_refined 0.183
r_dihedral_angle_2_deg 42.313
r_nbtor_refined 0.273
r_dihedral_angle_4_deg 16.943
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 640
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 53

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
ADSC data collection version: Quantum
DENZO data reduction
SCALEPACK data scaling
SHARP phasing