X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 295.0
Details PEG 400, cadmium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.99 α = 90
b = 45.99 β = 90
c = 52.99 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-04-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.9792 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
2 34.7 98.3 0.043 -- -- 8.8 2063 2063 0.0 0.0 41.3
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)
2.0 2.07 100.0 0.392 -- 6.5 9.2 199

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 2.0 34.7 0.0 0.0 2063 2063 284 98.3 0.23075 0.23075 0.22369 0.27629 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 1.999 2.051 137 17 120 0.303 0.371 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 54.231
Anisotropic B[1][1] 0.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.82
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 11.925
r_scbond_it 7.273
r_mcangle_it 4.165
r_mcbond_it 1.982
r_nbd_refined 0.32
r_gen_planes_refined 0.012
r_chiral_restr 0.245
r_dihedral_angle_4_deg 11.355
r_dihedral_angle_3_deg 24.811
r_dihedral_angle_2_deg 57.326
r_dihedral_angle_1_deg 7.392
r_angle_refined_deg 3.173
r_bond_refined_d 0.042
r_nbtor_refined 0.34
r_xyhbond_nbd_refined 0.03
r_metal_ion_refined 0.637
r_symmetry_vdw_refined 0.364
r_symmetry_hbond_refined 0.371
r_symmetry_metal_ion_refined 0.202
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 237
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 5

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement