X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details 0.1M Sodium Acetate, 0.8M Ammonium Sulfate, 40mM Cadmium Chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.25 α = 90
b = 72.25 β = 90
c = 94.26 γ = 90
Symmetry
Space Group P 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200HB 1.5418 -- --

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 15 95.0 -- 0.0602 -- 3.2 18325 17408 2.0 -- 17.612
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 -- 95.1 -- 0.092 -- 4.9 961

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 15.0 -- -- -- 18325 988 95.36 0.24 0.21981 0.2191 0.23339 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 1.9 1.949 961 74 1256 0.24 0.303 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.612
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.17
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.078
r_dihedral_angle_1_deg 5.697
r_angle_refined_deg 1.19
r_symmetry_vdw_refined 0.523
r_mcbond_it 0.471
r_scangle_it 2.36
r_bond_refined_d 0.009
r_scbond_it 1.523
r_symmetry_hbond_refined 0.185
r_xyhbond_nbd_refined 0.109
r_mcangle_it 0.915
r_gen_planes_refined 0.004
r_nbd_refined 0.211
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.093
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1690
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 115

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing