2BZI | pdb_00002bzi

CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XWS	PDB ENTRY 1XWS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.241	α = 90
b = 98.241	β = 90
c = 80.891	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	100	IMAGE PLATE	MARRESEARCH	MIRRORS	2005-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	1.9	50	97.1	0.04	15.7	5.1		34129		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	1.9	2	97		0.24	3.4	2.9

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	PDB ENTRY 1XWS	1.9	40	31653	1709	95.1	0.218	0.216	0.22	0.265	0.27	RANDOM	22.54

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]
0.42	0.21		0.42		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.331
r_dihedral_angle_4_deg	15.212
r_dihedral_angle_3_deg	13.005
r_dihedral_angle_1_deg	5.489
r_scangle_it	5.081
r_scbond_it	3.233
r_mcangle_it	2.132
r_mcbond_it	1.27
r_angle_refined_deg	1.106
r_angle_other_deg	0.77
r_symmetry_vdw_refined	0.272
r_symmetry_vdw_other	0.264
r_nbd_refined	0.196
r_nbtor_refined	0.178
r_symmetry_hbond_refined	0.175
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.161
r_nbtor_other	0.081
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	2214
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing