X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details 2.000000000M (NH4)2SO4, 0.200000000M Li2SO4, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.89 α = 90
b = 98.89 β = 90
c = 170.79 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-05-13
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97936 SSRL BL9-2

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
1.97 49.44 100.0 0.131 -- -- -- -- 68965 -- -3.0 25.138
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)
1.97 2.05 100.0 0.966 -- 2.1 -- --

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 1.97 49.445 -- 0.0 -- 68909 3488 99.89 -- 0.16 0.158 0.191 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 1.97 2.021 -- 260 4743 0.234 0.279 -- 99.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.65
Anisotropic B[1][1] -0.48
Anisotropic B[1][2] -0.24
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.72
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_angle_other_deg 0.935
r_gen_planes_refined 0.006
r_dihedral_angle_2_deg 35.739
r_gen_planes_other 0.001
r_scbond_it 4.54
r_scangle_it 6.841
r_chiral_restr 0.089
r_angle_refined_deg 1.421
r_dihedral_angle_3_deg 12.662
r_bond_refined_d 0.015
r_mcbond_it 1.497
r_dihedral_angle_1_deg 5.483
r_mcangle_it 2.477
r_mcbond_other 0.632
r_dihedral_angle_4_deg 19.955
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4777
Nucleic Acid Atoms 0
Heterogen Atoms 139
Solvent Atoms 636

Software

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