X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapordiffusion Combined with Soaking with Inhibitor at 1 Mm Concentration
pH 9
Temperature 298.0
Details 40% MPD, pH 9.0, vapordiffusion, combined with soaking with inhibitor at 1 mM concentration, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.68 α = 90
b = 73.2 β = 90
c = 134.45 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 monochromator 2002-03-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.91 CHESS F1

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 20 96.7 0.091 0.091 -- 5.4 34179 34179 1.0 1.0 28.1
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)
2.0 2.07 98.9 0.37 0.37 5.8 -- --

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 2.0 20.0 0.0 0.0 34179 31608 1660 94.48 0.1685 0.16854 0.16709 0.19489 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 2.0 2.052 -- 120 2260 0.192 0.223 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 28.086
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_scangle_it 2.966
r_symmetry_hbond_refined 0.151
r_mcbond_it 0.661
r_nbd_refined 0.198
r_bond_refined_d 0.013
r_symmetry_vdw_refined 0.203
r_gen_planes_refined 0.005
r_angle_refined_deg 1.317
r_scbond_it 2.003
r_chiral_restr 0.096
r_dihedral_angle_1_deg 6.248
r_xyhbond_nbd_refined 0.12
r_mcangle_it 1.221
r_metal_ion_refined 0.02
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.188
Luzzati ESD (R-Free Set) 0.149
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3946
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 243

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.1.24