4LUR | pdb_00004lur

Crystal Structure of Zebrafish Interphotoreceptor Retinoid-Binding Protein (IRBP) Module 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J7X	PDB ENTRY 1J7X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	295	Protein solutions at a concentration of 20mg/ml were mixed with the reservoir solutions of 35-44% polyethylene glycol 8000 in 100mM HEPES pH 7.5 buffer containing 100mM NaBr in the 1:1, 2:1 and 3:1 volume ratios and vapor diffused against the reservoir solutions. Plate-shaped crystals appeared in about a week and continued to grow for a few more weeks., VAPOR DIFFUSION, SITTING DROP, temperature 295.K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.295	α = 90
b = 97.771	β = 90
c = 41.214	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315		2009-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979368, 0.979484, 0.9716932	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.9	50	99.6	0.085	40	6.8		27277

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.901	1.95	99.8		0.64	2.8	6.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD COMBINED WITH MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1J7X	1.9	50	27277	25467	1332	98.3	0.222	0.219	0.22	0.268	0.26	RANDOM	33.4

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]
-1.2			2.41		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.262
r_dihedral_angle_3_deg	15.58
r_dihedral_angle_4_deg	12.23
r_dihedral_angle_1_deg	5.711
r_scangle_it	4.008
r_scbond_it	2.51
r_mcangle_it	1.534
r_angle_refined_deg	1.374
r_mcbond_it	0.792
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2338
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	53

Software

Software
Software Name	Purpose
ADSC	data collection
CCP4	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing