X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details 2.400000000M (NH4)2SO4, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.68 α = 90
b = 75.68 β = 90
c = 132.1 γ = 90
Symmetry
Space Group P 43 21 2

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) 2010-04-07
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162,0.97935,0.97899 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
1.3 28.7 99.9 -- 0.084 -- 4.0 -- 94721 -- -- 11.259

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
MAD 1.3 28.699 -- 0.0 -- 94632 4739 99.87 -- 0.137 0.135 0.157 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 1.3 1.334 -- 326 6564 0.278 0.325 -- 99.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.479
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.925
r_scbond_it 3.779
r_angle_refined_deg 1.52
r_scangle_it 5.293
r_sphericity_free 7.395
r_rigid_bond_restr 1.835
r_gen_planes_refined 0.008
r_dihedral_angle_1_deg 6.752
r_mcbond_it 2.122
r_bond_refined_d 0.013
r_gen_planes_other 0.003
r_chiral_restr 0.092
r_angle_other_deg 1.127
r_dihedral_angle_3_deg 11.129
r_mcbond_other 1.343
r_sphericity_bonded 3.659
r_bond_other_d 0.003
r_dihedral_angle_2_deg 33.957
r_dihedral_angle_4_deg 21.573
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2467
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 444

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0110
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.3.15
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing