2HPS | pdb_00002hps

Crystal structure of coelenterazine-binding protein from Renilla Muelleri

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	2 microliter drops containing equal volumes of protein solution (12 mg/ml) and precipitate solution (0.5M ammonium sulfate, 0.1M sodium citrate dihydrate, 1M lithium sulfate monohydrate), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.948	α = 90
b = 55.948	β = 90
c = 292.202	γ = 120

Symmetry
Space Group	P 65 2 2

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	0.979	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	1.72	10	98.6	0.07	25.3	13		27912		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	1.72	1.78	87.7		0.33		2.4	2510

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	SAD	THROUGHOUT	1.72	10	27921	27912	1489	98.57	0.20024	0.20024	0.19879	0.2	0.22887	RANDOM	18.613

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]
0.03	0.02		0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.859
r_dihedral_angle_4_deg	12.576
r_dihedral_angle_3_deg	11.082
r_dihedral_angle_1_deg	4.249
r_scangle_it	3.148
r_scbond_it	2.358
r_angle_refined_deg	1.314
r_mcangle_it	1.166
r_mcbond_it	0.852
r_nbtor_refined	0.303
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.087
r_symmetry_hbond_refined	0.063
r_bond_refined_d	0.018
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1435
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SCA2STRUCTURE	phasing