X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 4.6
Temperature 292.0
Details 1 microliter of protein + 1 microliter of reservoir using streak seading, protein: 1mg/mL PFK, 10mM imidazol, 5mM mercaptoethanol, 10% glycerol, 10mM ATP, pH 7.0; reservoir: 0.7M ammonia sulfate, 0.1M sodium citrate pH 4.6, VAPOR DIFFUSION, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 161.66 α = 90
b = 188.3 β = 92.85
c = 231.56 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE Double crystal monochromator with 2 sets of mirrors 2009-03-13
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2

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
3.05 29.8 53.2 -- -- -- 97.5 -- 262877 1.0 1.0 75.78

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 3.05 29.8 -- 0.0 617625 255838 12864 -- 0.247 0.2019 0.2003 0.2318 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 3.05 3.13 -- 947 18092 0.2266 0.2664 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.17
Anisotropic B[1][1] -13.4997
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.0224
Anisotropic B[2][2] 9.7517
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.748
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 22.51
t_angle_deg 1.24
t_omega_torsion 2.58
t_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.529
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 64576
Nucleic Acid Atoms 0
Heterogen Atoms 449
Solvent Atoms 0

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
BUSTER refinement version: 2.8.0
XDS data reduction
XDS data scaling