X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 0.16M magnesium acetate, 20.0% Glycerol, 16.0% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.61 α = 90
b = 114.61 β = 90
c = 77.05 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2013-10-17
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 0.918401,0.979261,0.979152 ALS 8.2.1

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
1.57 29.39 99.1 0.076 -- -- -- -- 71815 -- -3.0 22.74
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)
1.57 1.63 94.7 0.947 -- 1.5 -- --

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 1.57 29.386 -- 0.0 -- 71742 3628 99.75 -- 0.1549 0.1541 0.1685 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 1.57 1.611 -- 236 4916 0.279 0.287 -- 98.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.1649
Anisotropic B[1][1] -0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.82
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_dihedral_angle_3_deg 11.527
r_angle_other_deg 0.695
r_mcangle_it 2.015
r_mcbond_it 1.224
r_dihedral_angle_1_deg 5.458
r_gen_planes_refined 0.004
r_angle_refined_deg 1.099
r_dihedral_angle_2_deg 37.487
r_chiral_restr 0.065
r_mcbond_other 1.223
r_bond_refined_d 0.005
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 12.63
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3656
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 480

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling
REFMAC refinement version: 5.7.0032
XDS data reduction
SHELXD phasing