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, ethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.94 α = 90
b = 46.94 β = 90
c = 111.54 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 0.97895 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
1.49 30 98.2 0.039 -- -- 3.1 39458 38748 -- -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)
1.49 1.54 99.5 0.196 -- 2.5 1.9 3918

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
MAD 1.49 30.0 -- 0.0 35363 33970 3785 96.06 0.18135 0.18135 0.17821 0.21002 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 1.49 1.57 5330 569 4766 0.201 0.239 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic temperature factors
Mean Isotropic B 17.19
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.978
r_scbond_it 3.015
r_mcangle_it 1.832
r_mcbond_it 1.03
r_symmetry_hbond_refined 0.156
r_symmetry_vdw_other 0.237
r_symmetry_vdw_refined 0.215
r_xyhbond_nbd_other 0.018
r_bond_refined_d 0.015
r_bond_other_d 0.002
r_angle_refined_deg 1.445
r_angle_other_deg 1.036
r_dihedral_angle_1_deg 3.481
r_dihedral_angle_2_deg 14.823
r_chiral_restr 0.083
r_gen_planes_refined 0.006
r_gen_planes_other 0.004
r_nbd_refined 0.232
r_nbd_other 0.192
r_xyhbond_nbd_refined 0.139
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1972
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 234

Software

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