X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details Ammonium Sulphate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.18 α = 90
b = 109.18 β = 90
c = 309.44 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 290
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 2001-03-08
Diffraction Radiation
Monochromator Protocol
Mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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
3.8 32.44 99.5 -- 0.179 -- 7.9 11420 11420 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)
3.8 3.94 99.5 -- 0.517 2.1 -- --

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 3.8 20.0 0.0 0.0 11420 10779 641 100.0 -- 0.23074 0.22843 0.27106 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 3.8 3.897 -- 54 762 0.246 0.264 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.322
Anisotropic B[1][1] 1.78
Anisotropic B[1][2] 0.89
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.67
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.941
r_dihedral_angle_1_deg 4.854
r_dihedral_angle_2_deg 21.065
r_xyhbond_nbd_other 0.153
r_scangle_it 6.33
r_nbd_other 0.299
r_chiral_restr 0.152
r_mcangle_it 2.444
r_symmetry_vdw_refined 0.16
r_bond_other_d 0.002
r_gen_planes_refined 0.006
r_symmetry_hbond_refined 0.415
r_bond_refined_d 0.024
r_mcbond_it 1.239
r_symmetry_vdw_other 0.205
r_gen_planes_other 0.005
r_nbd_refined 0.315
r_angle_refined_deg 2.338
r_xyhbond_nbd_refined 0.19
r_nbtor_other 0.629
r_scbond_it 3.362
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.5
Luzzati Resolution Cutoff (Low) 0.53
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3813
Nucleic Acid Atoms 0
Heterogen Atoms 109
Solvent Atoms 13

Software

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