X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.2
Temperature 298.0
Details 0.1 M Tris, 4 mM NiCl2,10 mM dTDP-D-xylose, 35% PEG 2000, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.85 α = 90
b = 140.87 β = 92.72
c = 53.7 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-10-28
Diffraction Radiation
Monochromator Protocol
Liquid gallium cooled, bent, triangulary Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1

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 50.79 91.8 0.126 0.117 -- 5.3 63995 63969 2.96 3.1 21.38
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 1.81 43.3 0.112 0.085 8.1 2.1 500

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 70.71 -- 2.574 87974 60716 3217 91.8 -- 0.16698 0.16445 0.21562 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 2436 121 2436 0.148 0.26 0.142 --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.913
Anisotropic B[1][1] -0.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.03
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.46
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.271
r_gen_planes_other 0.005
r_bond_other_d 0.003
r_symmetry_hbond_refined 0.35
r_mcbond_it 0.747
r_scbond_it 1.847
r_sphericity_free 2.886
r_nbd_other 0.256
r_nbtor_other 0.089
r_mcangle_it 1.294
r_bond_refined_d 0.014
r_gen_planes_refined 0.007
r_nbd_refined 0.196
r_sphericity_bonded 1.069
r_chiral_restr 0.103
r_angle_other_deg 0.911
r_symmetry_vdw_refined 0.289
r_dihedral_angle_1_deg 7.41
r_angle_refined_deg 1.577
r_rigid_bond_restr 1.119
r_xyhbond_nbd_refined 0.176
r_scangle_it 2.882
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.142
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6304
Nucleic Acid Atoms 0
Heterogen Atoms 138
Solvent Atoms 874

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
MOLREP phasing
REFMAC refinement version: 5.1.19
CCP4 data scaling version: (SCALA)