X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.7
Temperature 277.0
Details 0.2000M MgAcetate, 20.0000% PEG-3350, No Buffer pH 7.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.22 α = 90
b = 56.22 β = 90
c = 301.9 γ = 90
Symmetry
Space Group P 41 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 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 0.91162,0.97932,0.97918 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
1.5 29.24 100.0 0.106 0.106 -- 7.1 -- 79386 -- -- 15.094
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)
1.5 1.54 99.9 0.814 0.814 0.9 6.0 5708

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 1.5 29.235 -- 0.0 -- 79233 3978 99.97 -- 0.136 0.134 0.16 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 1.5 1.539 -- 287 5418 0.203 0.237 -- 99.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.753
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.62
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.016
r_chiral_restr 0.103
r_mcangle_it 2.53
r_bond_other_d 0.003
r_sphericity_bonded 2.989
r_rigid_bond_restr 1.339
r_angle_refined_deg 1.537
r_dihedral_angle_2_deg 32.279
r_angle_other_deg 1.328
r_gen_planes_other 0.002
r_gen_planes_refined 0.008
r_mcbond_it 1.811
r_dihedral_angle_1_deg 4.066
r_scbond_it 2.183
r_scangle_it 3.065
r_mcbond_other 0.872
r_sphericity_free 7.382
r_dihedral_angle_3_deg 10.436
r_dihedral_angle_4_deg 13.036
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3941
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 603

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
autoSHARP phasing