X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 23.8% polyethylene glycol 3000, 0.1M citric acid pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.24 α = 90
b = 73.51 β = 108.36
c = 53.54 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-08-07
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

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
1.64 29.77 98.4 0.094 0.094 -- 7.3 -- 35714 -- -- 20.084
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)
1.64 1.68 97.2 0.865 0.865 0.9 3.8 2621

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 1.64 29.775 -- 0.0 -- 35686 1784 98.15 -- 0.174 0.172 0.209 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 1.639 1.682 -- 136 2473 0.259 0.332 -- 96.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.186
Anisotropic B[1][1] 0.49
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.5
Anisotropic B[2][2] 0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.25
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.938
r_bond_refined_d 0.016
r_chiral_restr 0.091
r_dihedral_angle_3_deg 12.723
r_bond_other_d 0.002
r_scangle_it 7.518
r_scbond_it 4.947
r_dihedral_angle_2_deg 34.123
r_gen_planes_refined 0.007
r_gen_planes_other 0.003
r_mcbond_other 0.546
r_angle_other_deg 1.401
r_angle_refined_deg 1.506
r_dihedral_angle_4_deg 6.609
r_dihedral_angle_1_deg 5.526
r_mcbond_it 1.774
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2001
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 338

Software

Software
Software Name Purpose
REFMAC refinement version: 5.4.0069
PHENIX refinement
SOLVE phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction