X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 291.0
Details 0.1 M Tris, 20% (w/v) PEG 3000, 0.2 M calcium acetate, pH 7.0, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.15 α = 90
b = 90.15 β = 90
c = 148.62 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APEX II CCD -- 2011-08-05
Diffraction Radiation
Monochromator Protocol
QUAZAR MX MICROFOCUS SOURCE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.54 -- --

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
2.94 78.08 99.8 0.128 0.128 -- 7.4 15475 15444 0.0 0.0 --
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)
2.939 2.96 92.6 0.395 -- 2.14 3.61 174

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 2.939 78.08 0.0 0.0 15435 15379 765 99.64 0.2455 0.2455 0.2429 0.2961 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 2.939 3.016 -- 71 1045 0.299 0.378 -- 98.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.641
Anisotropic B[1][1] -0.9
Anisotropic B[1][2] -0.45
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.35
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 0.486
r_scangle_it 0.893
r_dihedral_angle_1_deg 4.774
r_gen_planes_refined 0.003
r_mcbond_it 0.269
r_mcangle_it 0.501
r_chiral_restr 0.065
r_dihedral_angle_2_deg 34.467
r_bond_refined_d 0.006
r_dihedral_angle_4_deg 14.664
r_angle_refined_deg 0.952
r_dihedral_angle_3_deg 14.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3696
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 72

Software

Software
Software Name Purpose
SAINT data scaling
XPREP data reduction version: 2008/2 for Windows
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
PROTEUM PLUS data collection version: PLUS
SAINT data reduction