X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 7.5
Temperature 289.0
Details 1.1-1.3 M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, SMALL TUBES, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.89 α = 90
b = 189.92 β = 109.27
c = 88.16 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-02-23
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX10.1 0.97976 SRS PX10.1

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
2.59 30 99.6 -- 0.064 -- 3.4 112937 107281 0.0 -3.0 --
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)
2.6 2.64 99.6 -- 0.358 3.89 3.3 --

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
FOURIER SYNTHESIS 2.59 29.59 -- -- 107281 107281 5654 99.29 -- 0.20958 0.20656 0.26577 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 2.595 2.662 -- 403 7636 0.309 0.374 -- 95.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.826
Anisotropic B[1][1] -1.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.36
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.71
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 0.851
r_nbd_refined 0.224
r_symmetry_vdw_refined 0.191
r_symmetry_hbond_refined 0.133
r_chiral_restr 0.096
r_dihedral_angle_1_deg 6.261
r_dihedral_angle_3_deg 21.501
r_nbtor_refined 0.312
r_mcbond_it 0.471
r_angle_refined_deg 1.341
r_gen_planes_refined 0.004
r_bond_refined_d 0.01
r_scangle_it 1.889
r_xyhbond_nbd_refined 0.158
r_dihedral_angle_4_deg 19.187
r_scbond_it 1.125
r_dihedral_angle_2_deg 37.841
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 2.723
Luzzati Sigma A (Observed) 0.296
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 26363
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 110

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
MAR345 data collection
DENZO data reduction
SCALEPACK data scaling
REFMAC phasing