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_scbond_it 2.003
r_bond_refined_d 0.013
r_angle_refined_deg 1.317
r_dihedral_angle_1_deg 6.248
r_chiral_restr 0.096
r_gen_planes_refined 0.005
r_nbd_refined 0.198
r_xyhbond_nbd_refined 0.12
r_metal_ion_refined 0.02
r_symmetry_vdw_refined 0.203
r_symmetry_hbond_refined 0.151
r_mcbond_it 0.661
r_mcangle_it 1.221
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection