X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details 20mM SODIUM CITRATE BUFFER, 20% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.72 α = 90
b = 32.51 β = 90.03
c = 72.16 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2001-06-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 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
1.2 30 96.5 -- 0.053 -- 8.9 70118 70118 0.0 -3.0 12.9
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 1.22 96.9 -- 0.13 -- -- --

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 1.2 29.24 -- 0.1 66544 66544 3573 97.9 0.19124 0.18963 0.18963 0.22108 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 1.201 1.232 -- 256 4791 0.195 0.202 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.133
Anisotropic B[1][1] -0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.08
Anisotropic B[2][2] 0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.36
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.911
r_chiral_restr 0.1
r_symmetry_hbond_refined 0.604
r_gen_planes_other 0.004
r_scangle_it 3.33
r_xyhbond_nbd_refined 0.296
r_nbd_other 0.236
r_mcbond_it 1.173
r_angle_other_deg 0.809
r_dihedral_angle_1_deg 5.084
r_bond_other_d 0.001
r_gen_planes_refined 0.008
r_symmetry_vdw_refined 0.555
r_scbond_it 2.171
r_rigid_bond_restr 1.242
r_bond_refined_d 0.011
r_nbd_refined 0.27
r_nbtor_other 0.149
r_xyhbond_nbd_other 0.177
r_dihedral_angle_2_deg 14.195
r_sphericity_bonded 2.375
r_symmetry_vdw_other 0.606
r_angle_refined_deg 1.783
r_sphericity_free 2.012
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.16
Luzzati Sigma A (Observed) 0.1
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.18
Luzzati Sigma A (R-Free Set) 0.09
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1902
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 541

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
MAR data reduction
SCALEPACK data scaling
CNS phasing