X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 297.0
Details 1.4M tri-sodium citrate dihydrate, pH 5.6-6.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.56 α = 90
b = 123.56 β = 90
c = 123.56 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-06-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9793 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
2.6 50 96.6 0.086 -- -- 2.8 -- 18960 -- -- --
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)
2.6 2.69 99.0 0.606 -- 2.0 2.8 2925

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 2.6 37.27 -- 0.0 -- 18887 961 96.68 -- 0.195 0.192 0.237 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 2.6 2.672 1413 68 1345 0.327 0.354 -- 98.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.238
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.02
r_scbond_it 2.723
r_mcangle_it 2.641
r_mcbond_it 1.474
r_symmetry_hbond_refined 0.124
r_bond_refined_d 0.011
r_angle_refined_deg 1.309
r_dihedral_angle_1_deg 5.387
r_dihedral_angle_2_deg 37.869
r_dihedral_angle_3_deg 16.617
r_dihedral_angle_4_deg 17.177
r_chiral_restr 0.081
r_gen_planes_refined 0.004
r_nbd_refined 0.219
r_nbtor_refined 0.304
r_xyhbond_nbd_refined 0.135
r_symmetry_vdw_refined 0.209
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2866
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 64

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 version: 5.2.0019 refinement