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_scangle_it 2.664
r_scbond_it 1.699
r_mcangle_it 0.92
r_mcbond_it 0.536
r_symmetry_hbond_refined 0.237
r_symmetry_vdw_refined 0.177
r_bond_refined_d 0.009
r_angle_refined_deg 1.088
r_dihedral_angle_1_deg 4.309
r_dihedral_angle_2_deg 35.662
r_dihedral_angle_3_deg 17.259
r_dihedral_angle_4_deg 13.05
r_chiral_restr 0.062
r_gen_planes_refined 0.004
r_nbd_refined 0.197
r_nbtor_refined 0.283
r_xyhbond_nbd_refined 0.161
r_metal_ion_refined 0.028
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

Computing
Computing Package Purpose
ADSC Quantum Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement