1S36

Crystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1modified microbatch7.52771.5 M tri-sodium citrate, 0.1 M Na-HEPES, pH 7.5, modified microbatch, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.445α = 90
b = 53.445β = 90
c = 144.032γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Rigaku/msc HiRes22002-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9672.4610.069.3714.9115775-315
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.962.050.970.192.111982

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1JF21.96501482378098.510.224590.222780.25922RANDOM16.388
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]
0.420.42-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.924
r_scangle_it3.421
r_scbond_it2.156
r_mcangle_it1.288
r_angle_refined_deg1.207
r_mcbond_it0.698
r_symmetry_vdw_refined0.214
r_nbd_refined0.198
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.924
r_scangle_it3.421
r_scbond_it2.156
r_mcangle_it1.288
r_angle_refined_deg1.207
r_mcbond_it0.698
r_symmetry_vdw_refined0.214
r_nbd_refined0.198
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.162
r_metal_ion_refined0.133
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1489
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
LSCALEdata scaling