X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details drop: 14 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 3.2% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.19 α = 90
b = 140.19 β = 90
c = 184.56 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 MARMOSAIC 300 mm CCD -- 2011-07-29
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D -- APS 21-ID-D

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
2.77 121.41 99.5 0.105 -- -- -- -- 53634 0.0 -3.0 59.93
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)
2.77 2.84 100.0 0.775 -- 2.14 -- --

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 2.77 19.9 -- -- -- 53634 2682 99.9 -- 0.192 0.191 0.227 --
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 2.77 2.84 -- 193 3673 0.269 0.319 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.0
Anisotropic B[1][1] 0.25
Anisotropic B[1][2] 0.13
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.044
r_scbond_it 2.639
r_mcangle_it 1.685
r_mcbond_it 0.91
r_gen_planes_refined 0.01
r_chiral_restr 0.148
r_dihedral_angle_4_deg 25.251
r_dihedral_angle_3_deg 20.015
r_dihedral_angle_2_deg 33.856
r_dihedral_angle_1_deg 7.406
r_angle_refined_deg 2.58
r_bond_refined_d 0.024
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6356
Nucleic Acid Atoms 0
Heterogen Atoms 462
Solvent Atoms 98

Software

Computing
Computing Package Purpose
refmac5 Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction