X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE IN 100MM HEPES BUFFER AT PH 7.5. PRECIPITANT WAS 16% POLYETHYLENE GLYCOL 5000MME. THE PROTEIN WAS INCUBATED WITH 1MM OF THE INHIBITOR PRIOR CRYSTALLISATION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.5 α = 90
b = 60.15 β = 90
c = 97.21 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 TOROIDAL MIRROR 1999-09-15
Diffraction Radiation
Monochromator Protocol
SILICON SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
1.7 50 93.9 0.055 -- -- 2.9 -- 33830 -- 0.0 --
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)
1.7 1.76 88.7 0.157 -- 5.8 2.7 --

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 1.7 50.0 -- -- -- 33830 1773 94.1 -- 0.129 0.127 0.168 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 1.7 1.74 -- 126 2288 0.146 0.208 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.09
Anisotropic B[1][1] -0.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.22
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.6
r_scbond_it 2.372
r_mcangle_it 1.535
r_mcbond_it 0.934
r_nbd_refined 0.225
r_gen_planes_other 0.005
r_gen_planes_refined 0.008
r_chiral_restr 0.103
r_dihedral_angle_4_deg 17.508
r_dihedral_angle_3_deg 11.374
r_dihedral_angle_2_deg 39.021
r_dihedral_angle_1_deg 5.279
r_angle_other_deg 2.143
r_angle_refined_deg 1.653
r_bond_other_d 0.002
r_bond_refined_d 0.014
r_nbd_other 0.285
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.1
r_symmetry_vdw_refined 0.167
r_symmetry_vdw_other 0.236
r_symmetry_hbond_refined 0.146
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2839
Nucleic Acid Atoms 0
Heterogen Atoms 95
Solvent Atoms 471

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.06 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.06 refinement
AMORE model building