X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details PEG 6000, sodium acetate, calcium chrolide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.23 α = 90
b = 40.23 β = 90
c = 343.47 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V -- 2000-05-19
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.02 SPRING-8 BL45PX

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
2 200 95.9 0.079 -- -- 7.6 12467 11956 -- 0.0 31.55
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)
2.0 2.07 98.0 0.27 -- -- -- 1149

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 2.0 20.0 -- 1.0 11722 11336 569 96.7 -- 0.22513 0.22308 0.26686 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 2.0 2.051 -- 44 809 0.238 0.294 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.144
Anisotropic B[1][1] 0.75
Anisotropic B[1][2] 0.37
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.12
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.138
r_nbd_refined 0.262
r_dihedral_angle_1_deg 3.101
r_nbd_other 0.228
r_angle_other_deg 0.87
r_metal_ion_refined 0.154
r_symmetry_vdw_refined 0.13
r_chiral_restr 0.1
r_mcangle_it 2.31
r_bond_other_d 0.001
r_scangle_it 5.497
r_scbond_it 3.384
r_angle_refined_deg 1.653
r_gen_planes_other 0.003
r_bond_refined_d 0.022
r_symmetry_vdw_other 0.216
r_mcbond_it 1.299
r_gen_planes_refined 0.007
r_xyhbond_nbd_refined 0.169
r_dihedral_angle_3_deg 14.455
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1225
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 86

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
AMoRE model building
SCALEPACK data reduction
DENZO data collection
REFMAC version: 5.0 refinement