X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.3
Temperature 296.0
Details ammonium sulfate, sodium acetate, BeCl2, NaF, MnCl2, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.3 α = 90
b = 91.3 β = 90
c = 200.35 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV osmic confocal mirrors --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
2.1 30 95.6 0.053 -- -- 5.2 104211 104211 0.0 0.0 --
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)
2.1 2.18 72.1 -- -- -- -- --

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 2.1 30.0 -- 0.0 104211 98990 5221 95.59 0.236 0.23733 0.23621 0.25828 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 2.1 2.18 -- -- 5317 -- -- -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model overall
Mean Isotropic B 29.428
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] -0.13
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.39
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.96
r_scbond_it 2.379
r_mcangle_it 1.636
r_mcbond_it 0.892
r_symmetry_hbond_refined 0.286
r_symmetry_vdw_other 0.317
r_symmetry_vdw_refined 0.241
r_xyhbond_nbd_other 0.12
r_xyhbond_nbd_refined 0.173
r_bond_refined_d 0.02
r_bond_other_d 0.003
r_angle_refined_deg 1.734
r_angle_other_deg 0.944
r_dihedral_angle_1_deg 4.157
r_dihedral_angle_2_deg 17.259
r_chiral_restr 0.102
r_gen_planes_refined 0.007
r_gen_planes_other 0.004
r_nbd_refined 0.247
r_nbd_other 0.214
r_nbtor_other 0.191
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13326
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 207

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement