4IKU

Crystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with 2-((5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)amino)-3-phenylpropanamide

X-RAY DIFFRACTION

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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
2.39	48.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.493	α = 90
b = 77.377	β = 90.76
c = 48.088	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	1.3	50	89	0.033	0.04	37.293	3.8	75896	75896	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	1.3	1.35	48.4		0.268	0.317	2.46	2.6	4103

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	1.3	34.02	2	75896	72035	3833	88.97	0.18972	0.18972	0.18896	0.20382	RANDOM	19.717

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]
0.03		-0.07	-0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.002
r_dihedral_angle_4_deg	12.918
r_dihedral_angle_3_deg	11.202
r_dihedral_angle_1_deg	5.936
r_rigid_bond_restr	4.377
r_scbond_it	3.988
r_sphericity_free	3.905
r_sphericity_bonded	3.511
r_scangle_it	3.228
r_mcangle_it	1.323
r_angle_refined_deg	1.107
r_mcbond_it	0.764
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.255
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.165
r_metal_ion_refined	0.153
r_xyhbond_nbd_refined	0.09
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2396
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	30

Software

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