X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 20mM Hepes/NaOH pH 7.5, 2mM MgCl2 and 2 mM DTT, set up for crystallization in 0.1 M Hepes/NaOH ph 7.5, 0.2 M CaCl2, 28% PEG 400, 5% glycerol, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.37 α = 90
b = 111.75 β = 90
c = 62.49 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-02-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA -- 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
1.2 50 99.9 -- 0.065 -- 8.3 90050 89939 -3.0 -3.0 15.46
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)
1.2 1.25 99.9 -- 0.551 4.4 7.9 10234

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 1.2 41.65 -- -- -- 85442 4497 100.0 -- 0.12481 0.12332 0.15322 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 1.2 1.231 -- 329 6254 0.145 0.181 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.554
Anisotropic B[1][1] 0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.39
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 2.454
r_dihedral_angle_4_deg 19.432
r_mcangle_it 3.42
r_angle_other_deg 1.634
r_chiral_restr 0.137
r_scbond_it 4.809
r_dihedral_angle_2_deg 34.254
r_gen_planes_refined 0.011
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 12.175
r_dihedral_angle_3_deg 11.604
r_sphericity_bonded 6.039
r_bond_other_d 0.001
r_mcbond_it 2.413
r_sphericity_free 15.257
r_bond_refined_d 0.026
r_mcbond_other 1.183
r_angle_refined_deg 2.184
r_scangle_it 6.626
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1887
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 435

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement version: 5.5.0070
XDS data reduction
XSCALE data scaling