3DYL | pdb_00003dyl

human phosphdiesterase 9 substrate complex (ES complex)

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
4.67	73.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.787	α = 90
b = 103.787	β = 90
c = 269.799	γ = 90

Symmetry
Space Group	P 41 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 210		2007-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ DW	1.5418	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	96.67				37247	37247		2

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	2.7	2.8	100		0.771	2	7.3	4075

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	2.7	96.67	37247	4216	99.72	0.19089	0.18757	0.19	0.21902	0.22	RANDOM	42.135

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]
2.06			2.06		-4.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.576
r_dihedral_angle_4_deg	21.117
r_dihedral_angle_3_deg	17.289
r_dihedral_angle_1_deg	6.055
r_scangle_it	3.421
r_scbond_it	2.318
r_angle_refined_deg	1.931
r_mcangle_it	1.262
r_angle_other_deg	1.118
r_mcbond_it	1.086
r_symmetry_vdw_other	0.292
r_nbd_refined	0.253
r_symmetry_vdw_refined	0.25
r_nbtor_refined	0.202
r_nbd_other	0.2
r_mcbond_other	0.186
r_xyhbond_nbd_refined	0.169
r_metal_ion_refined	0.169
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.106
r_nbtor_other	0.096
r_bond_refined_d	0.023
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5412
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement