4ALW | pdb_00004alw

Benzofuropyrimidinone Inhibitors of Pim-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		IN-HOUSE PIM1 STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2		pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
2.9	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.449	α = 90
b = 97.449	β = 90
c = 81.003	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	155	CCD	MARMOSAIC 325 mm CCD		2007-01-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	1.92	37.42	97.9	0.07	17.33	7.4		33275		-3

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	1.92	2.03	95.2		1.28	1.6	5.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	IN-HOUSE PIM1 STRUCTURE	1.92	37.42	31220	1670	98.32	0.15781	0.15516	0.15	0.20731	0.21	RANDOM	37.685

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	33.585
r_dihedral_angle_4_deg	17.316
r_dihedral_angle_3_deg	13.795
r_dihedral_angle_1_deg	6.771
r_scangle_it	6.036
r_scbond_it	4.345
r_mcangle_it	2.715
r_angle_refined_deg	2.238
r_mcbond_it	1.845
r_nbtor_refined	0.32
r_symmetry_hbond_refined	0.278
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.231
r_symmetry_vdw_refined	0.213
r_chiral_restr	0.191
r_bond_refined_d	0.031
r_gen_planes_refined	0.012
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2223
Nucleic Acid Atoms
Solvent Atoms	337
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing