X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) GLYCEROL) WITH WELL SOLUTION (1.4-1.6 M AMMONIUM SULFATE, 0.1 M NA-CITRATE PH 5.8, 20 MM B-MERCAPTOETHANOL). SERIALLY DILUTED CRUSHED CRYSTALS WERE USED FOR MICRO-SEEDING ONE DAY AFTER THE DROPS WERE SET UP. CRYSTALS APPEARED ONE DAY AFTER SEEDING AND GREW TO A MAXIMUM SIZE OF 120 X 800 UM WITHIN 10 DAYS. CRYSTALS WERE STABILIZED FOR 12 HOURS BY TRANSFER TO FRESH WELL SOLUTION. THEY WERE THEN CRYO-PROTECTED BY STEP-WISE TRANSFER INTO CRYO-BUFFER CONTAINING 1.6 M AMMONIUM SULFATE, 50 MM HEPES, PH 7.5, 100 MM NA-CITRATE, PH 5.8, 100 MM KCL, 50 MM DTT AND UP TO 20% (V/V) GLYCEROL. IT WAS FOUND THAT MN2+ IONS COULD REPLACE THE MG2+ REQUIRED FOR THE BINDING OF THDP TO THE ENZYME.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 145.38 α = 90
b = 145.38 β = 90
c = 69.5 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2003-03-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- APS 19-ID

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
1.9 23.79 93.1 0.106 -- -- 6.8 -- 61707 -- -3.0 12.2
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)
1.9 1.93 95.4 0.544 -- 3.7 6.6 --

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
OTHER 1.9 23.79 -- 0.0 -- 59317 1326 89.0 -- 0.161 0.161 0.2 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 1.9 2.02 -- 212 9372 0.206 0.229 0.016 87.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.6
Anisotropic B[1][1] 2.15
Anisotropic B[1][2] 1.76
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.3
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.16
c_scbond_it 2.18
c_mcangle_it 1.91
c_mcbond_it 1.3
c_improper_angle_d 1.15
c_bond_d 0.014
c_angle_deg 1.6
c_dihedral_angle_d 22.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5558
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 540

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS 1.1 Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS version: 1.1 model building