3KM4 | pdb_00003km4

Optimization of Orally Bioavailable Alkyl Amine Renin Inhibitors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D91	pdb entry 3D91

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		278	0.1M Tris-HCl pH=7.0-8.0, 0.2M (NH4)2SO4, 18-26%(w/v) PEG3350, 5mg/ml Renin, 1mM Inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.834	α = 90
b = 96.94	β = 90
c = 148.568	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	CCD	ADSC QUANTUM 315		2005-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.9000	APS	14-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.86	81.11	94	0.066	19.86	4.7	62269	62269

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.95	95.3		0.3194	3.69	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	pdb entry 3D91	1.9	50	62137	48486	2591	82.16	0.20334	0.20027	0.2	0.26135	0.26	RANDOM	28.111

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]
-1.39			2.07		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.828
r_dihedral_angle_3_deg	16.337
r_dihedral_angle_4_deg	13.319
r_dihedral_angle_1_deg	8.015
r_scangle_it	4.692
r_scbond_it	3.2
r_angle_refined_deg	2.119
r_mcangle_it	2.03
r_mcbond_it	1.231
r_symmetry_hbond_refined	0.383
r_nbtor_refined	0.321
r_xyhbond_nbd_refined	0.271
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.229
r_chiral_restr	0.145
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
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_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5167
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms	186

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling