X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 291.0
Details 0.8 M phosphate, 0.2 M sodium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.46 α = 90
b = 83.35 β = 90
c = 92.18 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 MARMOSAIC 225 mm CCD -- 2010-04-09
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2

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
1.42 40.33 98.4 -- -- -- -- -- 80074 0.0 2.0 --
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)
1.42 1.47 86.0 -- -- -- -- --

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
SIRAS 1.42 40.33 -- 0.0 79961 79961 4002 98.34 -- 0.14714 0.14545 0.17849 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 1.42 1.456 -- 230 4707 0.496 0.496 -- 83.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.845
Anisotropic B[1][1] 0.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.175
r_dihedral_angle_1_deg 6.094
r_sphericity_bonded 8.425
r_mcbond_it 2.747
r_dihedral_angle_4_deg 13.777
r_dihedral_angle_2_deg 37.34
r_gen_planes_refined 0.015
r_sphericity_free 14.313
r_dihedral_angle_3_deg 12.461
r_angle_refined_deg 2.229
r_bond_refined_d 0.03
r_scangle_it 6.321
r_scbond_it 4.787
r_mcangle_it 3.72
r_rigid_bond_restr 3.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2927
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 417

Software

Software
Software Name Purpose
MAR345dtb data collection
SHELX model building
REFMAC refinement version: 5.5.0110
DENZO data reduction
SCALEPACK data scaling
SHELX phasing