X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.2
Details CRYSTALS OF THE ENZYME-INHIBITOR COMPLEX WERE GROWN BY VAPOUR DIFFUSION METHOD AGAINST PRECIPITANT SOLUTION CONTAINING OF 38% MPD AND 0,05 M SODIUM ACETATE BUFFER PH 5.2. DROPLETS OF 10-15 MKL CONTAINING 25-30 MG/ML PROTEIN SOLUTION IN THE SAME BUFFER WERE MIXED BEFORE CRYSTALLISATION WITH EQUAL VOLUME OF PRECIPITANT SOLUTION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 144.3 α = 90
b = 144.3 β = 90
c = 133.8 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 291
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1992-11-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 -- EMBL/DESY, Hamburg X13

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
1.8 30 98.9 0.08 -- -- 5.5 -- 147702 -- 1.0 24.7
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)
1.8 1.83 96.1 0.31 -- 4.4 6.0 --

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 1.8 28.63 -- -- -- 139776 7370 100.0 -- 0.15035 0.14915 0.17314 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 1.8 1.847 -- 546 10184 0.2 0.242 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.867
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 37.233
r_angle_refined_deg 1.248
r_symmetry_metal_ion_refined 0.189
r_metal_ion_refined 0.195
r_gen_planes_refined 0.005
r_nbtor_refined 0.307
r_nbd_refined 0.202
r_dihedral_angle_1_deg 6.099
r_xyhbond_nbd_refined 0.115
r_mcbond_it 0.627
r_symmetry_vdw_refined 0.184
r_dihedral_angle_3_deg 11.905
r_mcangle_it 1.063
r_dihedral_angle_4_deg 14.806
r_scangle_it 2.896
r_bond_refined_d 0.01
r_scbond_it 1.793
r_chiral_restr 0.085
r_symmetry_hbond_refined 0.102
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10666
Nucleic Acid Atoms 0
Heterogen Atoms 187
Solvent Atoms 902

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing