X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 3.8
Temperature 300.0
Details 50mM Citric acid, 0.2M Ammonium sulfate, 3mM Sodium tungstenate, 10mg/ml Protein, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.77 α = 90
b = 46.81 β = 113.97
c = 71.87 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2007-09-13
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.97915 ESRF ID14-2

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 20 99.6 0.061 -- -- 3.51 -- 115663 -- -3.0 20.28
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 1.6 99.7 0.421 -- 3.1 -- --

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
SAD 1.5 19.96 -- 0.0 59035 59035 2983 99.5 -- 0.17774 0.17648 0.20117 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 -- 190 4048 0.204 0.275 -- 98.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.948
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.94
r_nbd_refined 0.244
r_xyhbond_nbd_refined 0.142
r_mcangle_it 1.639
r_dihedral_angle_1_deg 6.567
r_dihedral_angle_3_deg 13.269
r_nbtor_refined 0.309
r_dihedral_angle_4_deg 20.614
r_symmetry_hbond_refined 0.175
r_scangle_it 4.217
r_scbond_it 2.691
r_metal_ion_refined 0.884
r_bond_refined_d 0.014
r_angle_refined_deg 1.605
r_gen_planes_refined 0.008
r_symmetry_vdw_refined 0.209
r_chiral_restr 0.104
r_dihedral_angle_2_deg 31.093
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3261
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 225

Software

Software
Software Name Purpose
XSCALE data scaling
SHELX phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.004
ProDC data collection
SHELXD phasing