X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.05 α = 90
b = 137.03 β = 90
c = 45.18 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-05-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0000 ESRF ID23-1

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
2.7 74.07 99.7 -- 0.139 4.688 3.8 15630 15630 -- -- 39.42
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)
2.7 2.85 99.6 0.55 0.55 1.3 3.9 2245

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
MOLECULAR REPLACEMENT 2.7 45.22 -- 0.0 -- 15605 773 99.5 -- 0.213 0.21 0.259 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 2.7 2.77 -- 47 1076 0.248 0.319 -- 99.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.81
Anisotropic B[1][1] -0.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.43
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 3.028
r_bond_refined_d 0.004
r_dihedral_angle_1_deg 5.385
r_dihedral_angle_3_deg 12.521
r_angle_other_deg 0.662
r_dihedral_angle_4_deg 10.614
r_mcbond_it 1.714
r_gen_planes_refined 0.003
r_gen_planes_other 0.001
r_chiral_restr 0.057
r_dihedral_angle_2_deg 32.401
r_bond_other_d 0.001
r_mcbond_other 1.712
r_angle_refined_deg 0.926
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 6
Solvent Atoms 15

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0032
SCALA data scaling version: 3.3.20
XDS data scaling
Coot model building
PDB_EXTRACT data extraction version: 3.14