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_scangle_it 0.893
r_scbond_it 0.486
r_mcangle_it 0.501
r_mcbond_it 0.269
r_gen_planes_refined 0.003
r_chiral_restr 0.065
r_dihedral_angle_4_deg 14.664
r_dihedral_angle_3_deg 14.55
r_dihedral_angle_2_deg 34.467
r_dihedral_angle_1_deg 4.774
r_angle_refined_deg 0.952
r_bond_refined_d 0.006
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

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
SAINT Data Reduction (intensity integration)
XPREP Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
XPREP version: 2008/2 for Windows data reduction
SAINT data collection