4GMV
Crystal Structure of the coiled-coil, RA and PH domains of Lamellipodin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3TCA | PDB ENTRY 3TCA |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 50 mM sodium formate, 20% (w/v) polyethylene glycol 3350, 30% (v/v) ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.63 | 53.27 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 117.617 | α = 90 |
b = 96.972 | β = 126.99 |
c = 76.824 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
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 | MAR CCD 165 mm | 2012-06-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4C | 0.97915 | NSLS | X4C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.4 | 38 | 95.4 | 24426 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.4 | 2.44 | 79.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 3TCA | 2.403 | 37.96 | 24426 | 1285 | 95.57 | 0.2421 | 0.23991 | 0.28254 | RANDOM | 50.181 |
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] | |
-0.02 | -0.03 | -0.02 | 0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.194 |
r_dihedral_angle_4_deg | 19.774 |
r_dihedral_angle_3_deg | 17.352 |
r_dihedral_angle_1_deg | 5.79 |
r_angle_refined_deg | 1.151 |
r_chiral_restr | 0.081 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4345 |
Nucleic Acid Atoms | |
Solvent Atoms | 101 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
MAR345dtb | data collection |
ARP/wARP | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |