X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 0.14 M Sodium malonate, 0.07 M Bis-Tris-Propane pH 7.5, 14 % PEG 3350, 7 % Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.37 α = 90
b = 98.37 β = 90
c = 81.33 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2007-12-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.97912 SLS X10SA

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
2.1 50 100.0 0.126 0.126 -- 3.8 26203 26203 -- 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)
2.1 2.18 100.0 0.724 -- -- 3.8 2592

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 2.1 36.71 -- 0.0 26168 26168 1330 99.95 0.166 0.166 0.164 0.206 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 2.1 2.154 -- 97 1805 0.229 0.298 -- 99.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.425
Anisotropic B[1][1] 0.12
Anisotropic B[1][2] 0.06
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.18
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 32.886
r_angle_other_deg 1.653
r_scbond_it 5.51
r_mcangle_it 3.4
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 17.488
r_gen_planes_other 0.001
r_angle_refined_deg 1.477
r_mcbond_other 0.638
r_dihedral_angle_3_deg 14.065
r_bond_other_d 0.002
r_chiral_restr 0.089
r_mcbond_it 2.196
r_dihedral_angle_1_deg 6.494
r_gen_planes_refined 0.008
r_scangle_it 7.364
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2263
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 217

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
CrystalClear data collection
HKL-2000 data reduction