3NDC
Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1CBF | PDB ENTRY 1CBF |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 292 | 0.1M Hepes pH 7.5, 10% isopropanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.66 | 53.79 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 84.517 | α = 90 |
b = 84.517 | β = 90 |
c = 144.637 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 65 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2007-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | 1.117 | SRS | PX10.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | 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 | 2 | 42.26 | 100 | 0.068 | 0.068 | 19.2 | 9.8 | 39472 | 39472 | 33.23 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.11 | 100 | 0.62 | 0.62 | 3.3 | 8.5 | 5720 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1CBF | 2 | 40.56 | 37436 | 37425 | 1979 | 99.97 | 0.18875 | 0.18694 | 0.2219 | RANDOM | 36.858 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.865 |
r_dihedral_angle_4_deg | 16.904 |
r_dihedral_angle_3_deg | 12.855 |
r_dihedral_angle_1_deg | 6.07 |
r_scangle_it | 2.947 |
r_scbond_it | 1.794 |
r_mcangle_it | 1.362 |
r_angle_refined_deg | 1.344 |
r_mcbond_it | 0.754 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3435 |
Nucleic Acid Atoms | |
Solvent Atoms | 219 |
Heterogen Atoms | 52 |
Software
Software | |
---|---|
Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |