X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.4
Details 4 MG/ML PROTEIN, 1 MM UMA, 5 MM AMP-PNP, 1 MM NAN3, 1 MM DTT, 20 MM HEPES, PH 7.4, 1.8 M NA-MALONATE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.44 α = 90
b = 89.84 β = 90
c = 108.54 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- 2008-04-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 -- ESRF ID29

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
1.9 46.46 98.2 0.06 -- -- 5.4 -- 51890 -- 3.0 37.009
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)
1.9 2.01 94.8 0.62 -- 3.22 5.5 --

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 1.9 46.47 -- -- -- 48594 2561 98.57 -- 0.19982 0.19809 0.23227 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 1.9 1.949 -- 174 3479 0.411 0.463 -- 97.21
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.207
Anisotropic B[1][1] -1.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.79
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.492
r_gen_planes_refined 0.009
r_mcbond_it 1.97
r_chiral_restr 0.121
r_dihedral_angle_2_deg 37.133
r_mcangle_it 2.622
r_scbond_it 3.087
r_dihedral_angle_4_deg 16.115
r_dihedral_angle_3_deg 13.906
r_bond_refined_d 0.011
r_dihedral_angle_1_deg 7.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3254
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 269

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0032
XDS data reduction
XSCALE data scaling
PHASER phasing