5X72 | pdb_00005x72

The crystal Structure PDE delta in complex with (rac)-p9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JV6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.568	α = 90
b = 55.568	β = 90
c = 115.465	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	AREA DETECTOR	ADSC QUANTUM 315r		2015-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97915	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.95	50	99.7	0.066	0.019	38.61	13.9		15663

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	100		0.481	0.132	7.4	14.2

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	4JV6	1.95	48.12	14524	742	97.37	0.18968	0.18748	0.2	0.23142	0.23	RANDOM	27.645

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]
-0.12	-0.06		-0.12		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.947
r_dihedral_angle_4_deg	14.844
r_dihedral_angle_3_deg	13.523
r_dihedral_angle_1_deg	7.572
r_long_range_B_refined	6.072
r_long_range_B_other	6.07
r_scangle_other	3.481
r_scbond_it	2.184
r_scbond_other	2.182
r_mcangle_it	2.168
r_mcangle_other	2.166
r_angle_refined_deg	2.089
r_mcbond_other	1.373
r_mcbond_it	1.372
r_angle_other_deg	0.971
r_chiral_restr	0.131
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1212
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	48

Software

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