X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 0.1M MgSO4, Peg 5000 MME 18%, 0.1M Mes pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.54 α = 90
b = 89.54 β = 90
c = 89.54 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2012-12-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.97628 ESRF ID23-2

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
1.5 44.77 100.0 -- -- -- -- 38574 38574 1.0 1.0 --
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)
1.5 1.58 100.0 0.342 -- -- -- --

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 1.5 44.77 -- -- -- 36594 1927 99.99 -- 0.13459 0.13287 0.16616 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 1.5 1.539 -- 120 2692 0.11 0.176 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.079
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 11.2
r_sphericity_bonded 8.091
r_dihedral_angle_1_deg 4.762
r_chiral_restr 0.065
r_mcbond_other 1.359
r_mcbond_it 1.358
r_angle_other_deg 0.747
r_gen_planes_other 0.001
r_sphericity_free 27.881
r_mcangle_it 1.677
r_dihedral_angle_4_deg 14.182
r_angle_refined_deg 1.115
r_rigid_bond_restr 1.735
r_bond_refined_d 0.007
r_dihedral_angle_2_deg 37.618
r_scbond_it 2.208
r_bond_other_d 0.001
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1551
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 291

Software

Software
Software Name Purpose
DNA data collection
PHASER phasing
REFMAC refinement version: 5.7.0032
MOSFLM data reduction
SCALA data scaling