2HQ8 | pdb_00002hq8

Crystal structure of coelenterazine-binding protein from renilla muelleri in the ca loaded apo form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	SITTING DROP VAPOR DIFFUSION USING 0.5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (13.5 MG/ML) AND RESERVOIR SOLUTION CONTAING 2% PEG 4000, 2.0M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, VAPOR DIFFUSION, temperature 291K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.414	α = 90
b = 78.414	β = 90
c = 125.001	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 300 mm CCD	ROSENBAUM	2005-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.54	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	10	100	0.042	16.9	6.7	39679	37300		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	84.4		0.32		2.7	3425

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	S,CA-SAS	THROUGHOUT	1.8	10	37300	37300	2079	100	0.20697	0.20697	0.20473	0.2	0.24747	RANDOM	21.749

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]
0.48	0.24		0.48		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.311
r_dihedral_angle_4_deg	19.456
r_dihedral_angle_3_deg	14.348
r_dihedral_angle_1_deg	8.563
r_scangle_it	4.258
r_scbond_it	2.832
r_mcangle_it	1.572
r_angle_refined_deg	1.459
r_mcbond_it	0.988
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.311
r_dihedral_angle_4_deg	19.456
r_dihedral_angle_3_deg	14.348
r_dihedral_angle_1_deg	8.563
r_scangle_it	4.258
r_scbond_it	2.832
r_mcangle_it	1.572
r_angle_refined_deg	1.459
r_mcbond_it	0.988
r_nbtor_refined	0.303
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.159
r_metal_ion_refined	0.118
r_chiral_restr	0.116
r_symmetry_hbond_refined	0.079
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2798
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCA2STRUCTURE	model building
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SCA2STRUCTURE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.