X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details PEG 4000, sodium acetate, n-propanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.98 α = 90
b = 46.98 β = 90
c = 111.46 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-1 Mirrors 2002-02-21
Diffraction Radiation
Monochromator Protocol
SI 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97857 APS 19-BM

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
1.45 30 98.7 0.041 -- -- 4.1 42743 42187 -- -3.0 --
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)
1.45 1.5 98.9 0.22 -- 3.2 3.4 4216

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 1.45 30.0 -- 0.0 38346 37127 4194 96.83 0.17645 0.17645 0.17413 0.19743 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 1.45 1.528 5814 597 5228 0.196 0.211 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic temperature factors
Mean Isotropic B 14.482
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.668
r_scbond_it 2.799
r_mcangle_it 1.753
r_mcbond_it 0.989
r_symmetry_hbond_refined 0.192
r_symmetry_vdw_other 0.222
r_symmetry_vdw_refined 0.114
r_bond_refined_d 0.023
r_bond_other_d 0.001
r_angle_refined_deg 1.679
r_angle_other_deg 0.831
r_dihedral_angle_1_deg 3.752
r_dihedral_angle_2_deg 14.981
r_chiral_restr 0.101
r_gen_planes_refined 0.008
r_gen_planes_other 0.003
r_nbd_refined 0.237
r_nbd_other 0.194
r_xyhbond_nbd_refined 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1972
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 246

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement