X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.8
Temperature 295.0
Details 0.1M sodium citrate, 5% Jeffamine M-600, 0.05M zinc acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.7 α = 90
b = 51.7 β = 90
c = 99.79 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-11-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.97912 NSLS X4A

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 51.7 99.7 0.061 -- -- 5.0 20545 20545 0.0 0.0 27.8
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 1.97 99.9 0.484 -- 3.4 5.0 2048

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 1.9 51.71 0.0 0.0 20545 20545 1054 99.71 0.19347 0.19347 0.19108 0.24028 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 1.901 1.95 1485 86 1399 0.214 0.25 -- 99.87
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic with TLS group assigned for each peptide chain.
Mean Isotropic B 37.479
Anisotropic B[1][1] 0.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.26
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 13.05
r_xyhbond_nbd_refined 0.161
r_symmetry_hbond_refined 0.237
r_chiral_restr 0.062
r_mcangle_it 0.92
r_metal_ion_refined 0.028
r_dihedral_angle_3_deg 17.259
r_dihedral_angle_1_deg 4.309
r_nbd_refined 0.197
r_nbtor_refined 0.283
r_symmetry_vdw_refined 0.177
r_dihedral_angle_2_deg 35.662
r_angle_refined_deg 1.088
r_bond_refined_d 0.009
r_scangle_it 2.664
r_gen_planes_refined 0.004
r_mcbond_it 0.536
r_scbond_it 1.699
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2045
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 99

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
ADSC data collection version: Quantum
DENZO data reduction
SCALEPACK data scaling
PHASER phasing