X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.4
Temperature 298.0
Details MK-2 protein at 5 mg/ml is equilibrated against a well solution of 1.6 - 2.0 M Sodium malonate at pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 255.55 α = 90
b = 255.55 β = 90
c = 255.55 γ = 90
Symmetry
Space Group F 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2005-03-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID

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
3.7 29.51 85.6 0.084 -- -- 5.1 -- 6885 -- -- --
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)
3.7 3.83 90.5 0.37 -- -- 5.0 --

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 3.8 29.51 -- -- -- 6091 294 85.13 -- 0.33074 0.32805 0.38827 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 3.801 3.899 -- 25 459 0.444 0.515 -- 89.63
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 80.0
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 0.638
r_gen_planes_refined 0.006
r_dihedral_angle_4_deg 16.315
r_angle_refined_deg 1.539
r_mcbond_it 0.493
r_dihedral_angle_2_deg 41.58
r_dihedral_angle_1_deg 6.849
r_chiral_restr 0.085
r_bond_refined_d 0.011
r_scangle_it 1.183
r_dihedral_angle_3_deg 22.621
r_mcangle_it 0.9
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2298
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
ADSC data collection version: Quantum
HKL-2000 data reduction
AMoRE phasing