5C3K | pdb_00005c3k

Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OPY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1M Hepes-NaOH 7.5, 3.9M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.616	α = 90
b = 71.616	β = 90
c = 105.104	γ = 90

Symmetry
Space Group	P 41 2 2

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	RIGAKU SATURN 70		2009-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	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	2.01	59.18	99	0.082	8.5	3	18705	18705		2.2

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	2.01	2.08	99.5		0.348	2.2

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	2OPY	2.02	59.18	17321	962	97.71	0.2192	0.21696	0.22	0.25995	0.26	RANDOM	41.124

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]
-0.26			-0.26		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.546
r_dihedral_angle_3_deg	17.843
r_dihedral_angle_4_deg	14.511
r_long_range_B_refined	7.38
r_long_range_B_other	7.37
r_dihedral_angle_1_deg	5.865
r_scbond_it	3.146
r_scbond_other	3.143
r_mcbond_it	2.163
r_angle_refined_deg	1.427
r_angle_other_deg	0.586
r_chiral_restr	0.117
r_bond_refined_d	0.011
r_bond_other_d	0.006
r_gen_planes_refined	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_scangle_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	866
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing