X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Temperature 291.0
Details 20% (w/v) PEG 8000, 0.2 M MgCl2 and 0.1 M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.5 α = 90
b = 93.5 β = 90
c = 137.07 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2009-08-08
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

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
2.67 80.97 99.8 0.101 0.101 -- 7.2 -- 20223 -- 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)
2.67 2.81 100.0 0.416 0.416 1.7 7.2 --

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 2.67 68.54 -- -- 24605 19135 1028 99.6 -- 0.198 0.195 0.253 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 2.67 2.74 -- 74 1387 0.373 0.399 -- 99.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.3
Anisotropic B[1][1] -5.735
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.735
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.47
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.317
r_scbond_it 2.554
r_mcangle_it 1.736
r_mcbond_it 0.897
r_gen_planes_refined 0.011
r_chiral_restr 0.084
r_dihedral_angle_4_deg 22.894
r_dihedral_angle_3_deg 18.074
r_dihedral_angle_2_deg 33.84
r_dihedral_angle_1_deg 5.844
r_angle_refined_deg 1.406
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3693
Nucleic Acid Atoms 0
Heterogen Atoms 208
Solvent Atoms 31

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 refinement
Phaser version: 1.3.3 molecular replacement
SCALA version: 3.2.25 data processing