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 CCD 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_nbd_other 0.285
r_symmetry_vdw_other 0.236
r_dihedral_angle_2_deg 39.021
r_angle_other_deg 2.143
r_dihedral_angle_1_deg 5.279
r_xyhbond_nbd_refined 0.1
r_angle_refined_deg 1.653
r_mcbond_it 0.934
r_dihedral_angle_4_deg 17.508
r_symmetry_vdw_refined 0.167
r_bond_other_d 0.002
r_bond_refined_d 0.014
r_gen_planes_other 0.005
r_scangle_it 3.6
r_dihedral_angle_3_deg 11.374
r_gen_planes_refined 0.008
r_chiral_restr 0.103
r_mcangle_it 1.535
r_scbond_it 2.372
r_symmetry_hbond_refined 0.146
r_nbd_refined 0.225
r_nbtor_other 0.088
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

Software
Software Name Purpose
REFMAC refinement version: 5.1.06
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing