4IKS | pdb_00004iks

Crystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with N1-(5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)-N2-(6-(trifluoromethyl)pyridin-2-yl)ethane-1,2-diamine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	6% PEG 10000, 100mM HEPES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.219	α = 90
b = 77.332	β = 92.36
c = 47.153	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315		2007-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.00	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	50	92	0.035	0.051	24.4	4	34271	34271	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	65.1		0.2406	0.3	2.92	3.5	2406

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.7	47.19	2	34271	30814	3447	91.92	0.1876	0.1876	0.1844	0.18	0.21552	0.21	RANDOM	21.478

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]
			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.571
r_dihedral_angle_4_deg	17.5
r_dihedral_angle_3_deg	14.313
r_dihedral_angle_1_deg	6.278
r_scangle_it	3.475
r_scbond_it	2.202
r_mcangle_it	1.378
r_angle_refined_deg	1.337
r_mcbond_it	0.768
r_symmetry_hbond_refined	0.386

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.571
r_dihedral_angle_4_deg	17.5
r_dihedral_angle_3_deg	14.313
r_dihedral_angle_1_deg	6.278
r_scangle_it	3.475
r_scbond_it	2.202
r_mcangle_it	1.378
r_angle_refined_deg	1.337
r_mcbond_it	0.768
r_symmetry_hbond_refined	0.386
r_nbtor_refined	0.307
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.174
r_metal_ion_refined	0.134
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2396
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.