5Y9Z | pdb_00005y9z

Crystal structure of rat hematopoietic prostaglandin D synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PD2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	8.5	293	50 mM Tris-HCl, pH 8.5, 35% PEG6000, 5 mM DTT, 5mM GSH, 2 mM Dioxane, 2 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.54	α = 90
b = 79.84	β = 90
c = 96.6	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2015-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.8	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.09	48.3	99.6	0.039	0.042	0.014	1	12.5	7.7		175007

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.09	1.11	99.5		0.529	0.568	0.201	0.929		7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1PD2	1.09	48.3	166098	8782	99.5	0.1567	0.1555	0.165	0.1786	0.1849	RANDOM	12.662

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]
0.52			-0.08		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.88
r_sphericity_free	21.73
r_dihedral_angle_4_deg	12.846
r_dihedral_angle_3_deg	11.254
r_sphericity_bonded	6.965
r_dihedral_angle_1_deg	5.305
r_rigid_bond_restr	1.937
r_angle_refined_deg	1.416
r_angle_other_deg	0.937
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3280
Nucleic Acid Atoms
Solvent Atoms	523
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data collection
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction