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_scangle_it 2.36
r_bond_refined_d 0.009
r_angle_refined_deg 1.19
r_dihedral_angle_1_deg 5.697
r_chiral_restr 0.078
r_gen_planes_refined 0.004
r_nbd_refined 0.211
r_xyhbond_nbd_refined 0.109
r_symmetry_vdw_refined 0.523
r_symmetry_hbond_refined 0.185
r_mcbond_it 0.471
r_mcangle_it 0.915
r_scbond_it 1.523
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement