X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 20-30% PEG 4K, 0.2 imidazole/malate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 30.56 α = 104.99
b = 51.79 β = 94.36
c = 79.78 γ = 94.85
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-10-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3

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
1.37 25 94.0 -- 0.022 -- 1.8 -- 92547 -- -- 14.7

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 1.37 25.0 -- 0.0 -- 90689 1843 93.97 -- 0.1531 0.15256 0.1797 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 1.37 1.405 -- 129 6486 0.209 0.228 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.992
Anisotropic B[1][1] 1.71
Anisotropic B[1][2] 0.49
Anisotropic B[1][3] -0.12
Anisotropic B[2][2] -0.95
Anisotropic B[2][3] 0.03
Anisotropic B[3][3] -0.68
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.089
r_nbd_other 0.264
r_nbd_refined 0.178
r_gen_planes_other 0.004
r_gen_planes_refined 0.007
r_chiral_restr 0.083
r_dihedral_angle_1_deg 6.844
r_angle_other_deg 0.801
r_angle_refined_deg 1.398
r_bond_other_d 0.002
r_bond_refined_d 0.011
r_xyhbond_nbd_refined 0.168
r_symmetry_vdw_refined 0.271
r_symmetry_vdw_other 0.324
r_symmetry_hbond_refined 0.186
r_mcbond_it 0.863
r_mcangle_it 1.549
r_scbond_it 2.071
r_scangle_it 3.117
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4437
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 589

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement