X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.15
Details ammonium dihydrogen, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.8 α = 90
b = 94.3 β = 90
c = 98.1 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 OXFORD PX210 -- --
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU

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
1.5 37.43 93.2 0.052 -- -- 5.6 -- 62367 1.0 1.0 14.6
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)
1.5 1.55 53.8 0.201 -- 2.7 1.7 3581

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
MOLECULAR REPLACEMENT 1.5 37.41 0.0 0.0 62367 62367 3152 92.5 -- -- 0.212 0.23 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 1.5 1.59 6885 359 6526 0.244 0.25 0.013 62.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 13.0
Anisotropic B[1][1] 0.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.48
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.4
c_scangle_it 2.77
c_bond_d 0.005
c_improper_angle_d 0.89
c_mcbond_it 1.01
c_dihedral_angle_d 23.4
c_mcangle_it 1.49
c_scbond_it 1.91
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3258
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 410

Software

Software
Software Name Purpose
d*TREK data scaling
d*TREK data reduction
CNS refinement
CNS phasing