4HXX | pdb_00004hxx

Pyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	14-20 % PEG monomethyl ether 2000, 100 mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.5	α = 90
b = 77.403	β = 90.92
c = 48.068	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	298	IMAGE PLATE	RIGAKU RAXIS IV		2010-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ DW	1.54

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	2.09	50	97.9	0.117	14.9	3.5		20262

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	2.09	2.16	86.6		0.49		3	1780

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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		THROUGHOUT	2.09	25.33	20226	1033	97.94	0.1936	0.1901	0.1909	0.2579	0.2554	RANDOM	43.0235

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]
1.78		1.5	-3.67		1.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.485
r_dihedral_angle_4_deg	16.728
r_dihedral_angle_3_deg	15.199
r_dihedral_angle_1_deg	6.603
r_scangle_it	3.884
r_scbond_it	2.54
r_mcangle_it	1.61
r_angle_refined_deg	1.551
r_mcbond_it	0.911
r_nbtor_refined	0.303
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.209
r_symmetry_hbond_refined	0.185
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.107
r_metal_ion_refined	0.102
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2396
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	49

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection