X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microgravity with Apcf Reactors
pH 6.5
Temperature 295.0
Details tris HCl, CaCl2, NaNO3, pH 6.5, Microgravity with APCF reactors, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.72 α = 90
b = 67.72 β = 90
c = 101.62 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 2000-10-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.91 EMBL/DESY, HAMBURG X11

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
1.08 20 99.5 -- 0.047 -- 15.32 101462 101462 -3.0 -3.0 4.5
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)
1.08 1.12 99.0 -- 0.234 5.61 -- 11322

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 1.08 20.0 0.0 0.0 -- 101462 1015 99.65 -- 0.11994 0.11974 0.13993 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 1.08 1.107 -- 83 7161 0.149 0.16 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 7.213
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.851
r_sphericity_free 2.615
r_rigid_bond_restr 0.882
r_scangle_it 2.998
r_scbond_it 1.965
r_mcangle_it 1.336
r_mcbond_it 0.814
r_symmetry_hbond_refined 0.23
r_symmetry_vdw_other 0.307
r_symmetry_vdw_refined 0.211
r_bond_refined_d 0.008
r_bond_other_d 0.003
r_angle_refined_deg 1.411
r_angle_other_deg 1.017
r_dihedral_angle_1_deg 6.295
r_chiral_restr 0.132
r_gen_planes_refined 0.006
r_gen_planes_other 0.003
r_nbd_refined 0.243
r_nbd_other 0.258
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.16
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.05
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2076
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 452

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