4IKR

Crystal structure of Type 1 human methionine aminopeptidase in complex with 2-(4-(5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)piperazin-1-yl)ethanol

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
2.38	48.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.345	α = 90
b = 77.423	β = 91.03
c = 48.023	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 8.2.1	1.00	ALS	8.2.1

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	1.78	50	93			30215	30215	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	1.8	1.86	69		0.24	0.29	2.71	2.9	2234

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.78	40.39	2	30215	28936	1510	91.43	0.18203	0.18203	0.18044	0.21124	RANDOM	23.118

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.387
r_dihedral_angle_4_deg	14.402
r_dihedral_angle_3_deg	12.6
r_dihedral_angle_1_deg	6.187
r_scangle_it	3.626
r_scbond_it	2.311
r_angle_refined_deg	1.441
r_mcangle_it	1.412
r_mcbond_it	0.796
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.387
r_dihedral_angle_4_deg	14.402
r_dihedral_angle_3_deg	12.6
r_dihedral_angle_1_deg	6.187
r_scangle_it	3.626
r_scbond_it	2.311
r_angle_refined_deg	1.441
r_mcangle_it	1.412
r_mcbond_it	0.796
r_nbtor_refined	0.305
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.2
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.099
r_metal_ion_refined	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2396
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	33

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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 R01GM133198.