3D48 | pdb_00003d48

Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BP3	FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.
experimental model	PDB	1F6F	FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.
experimental model	PDB	1RW5	FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.
experimental model	PDB	1N9D	FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	297	3.5M Sodium Chloride, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.35	α = 90
b = 125.35	β = 90
c = 69.82	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 225 mm CCD		2007-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0000	MAX II	I911-3

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	2.5	20	99.8	0.083	22.46	11.2	21763	21797	-3	-3	46.4

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)
	2.5	2.56	100		0.501	5.5	11.2	21797

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 (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.	2.5	20	21717	20629	1088	99.87	0.221	0.221	0.218	0.22	0.295	0.29	RANDOM	46.307

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]
-2.48	-1.24		-2.48		3.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.912
r_dihedral_angle_3_deg	22.244
r_dihedral_angle_4_deg	20.394
r_dihedral_angle_1_deg	8.69
r_scangle_it	4.035
r_scbond_it	2.465
r_angle_refined_deg	2.013
r_mcangle_it	1.782
r_mcbond_it	0.964
r_chiral_restr	0.133
r_bond_refined_d	0.02
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2945
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing