3HL8 | pdb_00003hl8

Crystal structure of exonuclease I in complex with inhibitor BCBP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C95	PDB entry 3C95

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	20 mg/mL Protein, 18-27% PEG 4000, 0.1-0.15 M MgCl2, Saturated inhibitor in DMSO soaked 4-5 days, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.823	α = 90
b = 91.966	β = 90
c = 106.28	γ = 90

Symmetry
Space Group	P 21 21 21

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		2007-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97869	APS	21-ID-D

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	1.55	50	93	0.071	34.5	5.7	72323	72323			19.9

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	1.55	1.61	85.9		0.36	2.69	2.1	6559

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 3C95	1.55	26.91	68067	68067	3594	92.76	0.1739	0.1739	0.17219	0.1729	0.20709	0.211	RANDOM	18.973

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]
1.07			-0.5		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.698
r_dihedral_angle_4_deg	14.775
r_dihedral_angle_3_deg	11.677
r_dihedral_angle_1_deg	5.479
r_sphericity_free	4.539
r_scangle_it	3.776
r_scbond_it	2.427
r_sphericity_bonded	2.413
r_mcangle_it	1.713
r_angle_refined_deg	1.361
r_rigid_bond_restr	1.194
r_mcbond_it	1.005
r_angle_other_deg	0.877
r_mcbond_other	0.403
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3702
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	41

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling