X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 60 mM Succinate (pH 5.5), 5.8 mM sodium pyruvate, 2.4 mM MnCl2, 450 mM KCl, and a range of 18 to 20% PEG 8000, 150 mM Alanine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.63 α = 95.15
b = 109.01 β = 93.45
c = 144.46 γ = 112.26
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing 2005-08-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 0.9795 NSLS X6A

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
1.65 100 92.5 0.074 -- -- 3.8 508417 508417 0.0 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)
1.65 1.71 55.2 0.314 -- 4.3 3.3 --

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 1.65 76.47 -- 0.0 508412 508412 25590 92.13 0.149 0.149 0.148 0.174 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 1.654 1.697 22458 1112 21346 0.188 0.237 -- 55.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.493
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.195
r_nbtor_refined 0.302
r_xyhbond_nbd_refined 0.126
r_chiral_restr 0.079
r_mcangle_it 0.918
r_gen_planes_refined 0.004
r_symmetry_vdw_refined 0.193
r_symmetry_hbond_refined 0.113
r_mcbond_it 0.491
r_scangle_it 3.005
r_dihedral_angle_2_deg 36.18
r_scbond_it 1.799
r_angle_refined_deg 1.151
r_dihedral_angle_3_deg 12.631
r_bond_refined_d 0.01
r_dihedral_angle_1_deg 5.0
r_dihedral_angle_4_deg 16.837
r_metal_ion_refined 0.085
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.195
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 31708
Nucleic Acid Atoms 0
Heterogen Atoms 422
Solvent Atoms 4794

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 1.701
MOLREP phasing