4NW7 | pdb_00004nw7

PDE4 catalytic domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM T-028-1 (COMPOUND #7) AGAINST JCSG_B9 OPTIMIZATION SCREEN 0.1M SODIUM CITRATE TRIBASIC / CITRIC ACID, PH 5.5, 19.45% W/V PEG 6,000, CRYO 20% ETHYLENE GLYCOL AND 0.1MM T-028-1, CRYSTAL TRACKING ID 232699H5, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.58	α = 90
b = 98.58	β = 90
c = 47.57	γ = 90

Symmetry
Space Group	P 42

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 300 mm CCD		2012-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07809	APS	21-ID-D

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	2.15	49.29	99.3	0.091	12.68	4	25192	25012		-3	32.32

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	2.15	2.21	99.3		0.505	3	4.1	1848

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.15	49.29	25192	25006	1274		0.158	0.155	0.17	0.207	0.21	RANDOM	28.71

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]
-0.36			-0.36		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.042
r_dihedral_angle_4_deg	17.612
r_dihedral_angle_3_deg	14.03
r_dihedral_angle_1_deg	5.294
r_mcangle_it	3.052
r_mcbond_it	2.085
r_mcbond_other	2.085
r_angle_refined_deg	1.595
r_angle_other_deg	0.953
r_chiral_restr	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	2710
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	54

Software

Software
Software Name	Purpose
MD2	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling