3MK6 | pdb_00003mk6

Substrate and Inhibitor Binding to Pank

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I7P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	Ammonium citrate dibasic, PEG 3350, and TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.709	α = 90
b = 180.38	β = 95.48
c = 77.419	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	MARMOSAIC 300 mm CCD		2007-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97921	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.98	50	98.8	0.086	17.5	3.6	106621	106621

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.98	2.05	90.2		0.473	1.8	2.7	9736

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	2I7P	1.98	50	100924	5292	99.06	0.18771	0.18541	0.185	0.23186	0.2298	RANDOM	33.417

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]
1.74		-0.37	-1.28		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.307
r_dihedral_angle_4_deg	17.087
r_dihedral_angle_3_deg	14.156
r_dihedral_angle_1_deg	5.358
r_scangle_it	3.737
r_scbond_it	2.435
r_mcangle_it	1.647
r_angle_refined_deg	1.462
r_mcbond_it	1.026
r_nbtor_refined	0.307
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.169
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10792
Nucleic Acid Atoms
Solvent Atoms	523
Heterogen Atoms	252

Software

Software
Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling