X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details 20.0000% PEG-1000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.09 α = 90
b = 62.45 β = 90
c = 120.27 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 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-03-19
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97922,0.97903 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
1.7 28.15 97.1 0.04 -- -- -- -- 42518 -- -3.0 19.609
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)
1.7 1.76 87.1 0.401 -- 1.7 -- --

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 1.7 28.149 -- 0.0 -- 42462 2131 98.59 -- 0.167 0.165 0.203 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 1.701 1.745 -- 142 2675 0.257 0.274 -- 90.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.293
Anisotropic B[1][1] -0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.63
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.903
r_dihedral_angle_1_deg 6.859
r_gen_planes_other 0.001
r_angle_refined_deg 1.543
r_dihedral_angle_3_deg 13.221
r_mcbond_other 0.592
r_bond_other_d 0.001
r_gen_planes_refined 0.007
r_scangle_it 6.847
r_chiral_restr 0.095
r_angle_other_deg 0.85
r_mcangle_it 2.953
r_scbond_it 4.762
r_bond_refined_d 0.016
r_dihedral_angle_2_deg 37.021
r_dihedral_angle_4_deg 14.103
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3258
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 409

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
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