1XP3 | pdb_00001xp3

Crystal Structure of Endonuclease IV (BA4508) from Bacillus anthracis at 2.57A Resolution.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	PEG 5000, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.886	α = 90
b = 55.39	β = 89.43
c = 64.972	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 4	Rh coated Si mirror	2004-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87000	SRS	PX9.6

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	2.57	50	93.7	0.061	14	2.7	10633	10633

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	2.57	2.66	86.6		0.242	4	2.5	964

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 1QTW	2.57	22.83	10606	10606	532	100	0.15478	0.15478	0.15117	0.16	0.22808	0.23	RANDOM	41.983

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]
-0.25		-0.12	0.2		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.336
r_dihedral_angle_4_deg	21.146
r_dihedral_angle_3_deg	18.13
r_dihedral_angle_1_deg	8.282
r_scangle_it	2.308
r_angle_refined_deg	1.649
r_scbond_it	1.468
r_angle_other_deg	0.939
r_mcangle_it	0.837
r_mcbond_it	0.656
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.208
r_nbd_other	0.198
r_symmetry_vdw_other	0.189
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.172
r_symmetry_vdw_refined	0.114
r_mcbond_other	0.113
r_chiral_restr	0.099
r_nbtor_other	0.092
r_metal_ion_refined	0.074
r_xyhbond_nbd_other	0.048
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2305
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing