3A4K

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E52	PDB ENTRY 2E52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	PEG3350, ammonium acetate, Magnesium ion, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.46	α = 90
b = 132.211	β = 111.03
c = 94.07	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	ADSC QUANTUM 4r	mirror	2006-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.000	Photon Factory	BL-6A

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	2.17	50	99.8	0.063	24.7	1.9		100664

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	2.17	2.23	98		0.404	3.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2E52	2.17	41.67	100399	5018	99.77	0.18	0.178	0.226	RANDOM	36.106

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]
0.05		0.53	0.51		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.522
r_dihedral_angle_3_deg	16.57
r_dihedral_angle_4_deg	15.567
r_dihedral_angle_1_deg	6.215
r_scangle_it	4.287
r_scbond_it	2.804
r_mcangle_it	1.829
r_angle_refined_deg	1.779
r_mcbond_it	0.969
r_chiral_restr	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.522
r_dihedral_angle_3_deg	16.57
r_dihedral_angle_4_deg	15.567
r_dihedral_angle_1_deg	6.215
r_scangle_it	4.287
r_scbond_it	2.804
r_mcangle_it	1.829
r_angle_refined_deg	1.779
r_mcbond_it	0.969
r_chiral_restr	0.12
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9775
Nucleic Acid Atoms	1462
Solvent Atoms	573
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.