2VCX | pdb_00002vcx

Complex structure of prostaglandin D2 synthase at 2.1A.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.4		PEG 6000 30%, TCEP 5MM, GSH 5MM, DIOXANE 1%, MGCL2 5MM, TRISHCL (PH8.4) 50 MM

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.813	α = 90
b = 123.813	β = 90
c = 106.297	γ = 90

Symmetry
Space Group	I 41

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 CCD	MIRRORS	2004-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.1	88	99.8	0.1	7.6	3.2		46651		1.8

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	2.1	2.15	100		0.1	1.8	3.2

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PD2	2.1	50	42575	2271	95.9	0.199	0.196	0.2	0.248	RANDOM	24.4

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]
0.31			0.31		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.317
r_dihedral_angle_4_deg	13.665
r_dihedral_angle_3_deg	12.046
r_dihedral_angle_1_deg	2.838
r_scangle_it	2.512
r_scbond_it	1.66
r_angle_refined_deg	1.37
r_mcangle_it	1.181
r_mcbond_it	0.709
r_nbtor_refined	0.31
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_metal_ion_refined	0.006
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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	6474
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	130

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing