2HOI | pdb_00002hoi

Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	MPD, SODIUM ACETATE, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.784	α = 90
b = 136.784	β = 90
c = 218.275	γ = 120

Symmetry
Space Group	P 32 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	MONOCHROMATOR	2003-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.078	ALS	8.2.1

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	2.601	19.92	81.49	0.09			72945	59441

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)
	2.601		81.64		0.198

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	1CRX	2.601	19.92	72945	59441	3007	81.49	0.2227	0.2227	0.184	0.19	0.246	0.25	RANDOM	30.818

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.021
r_dihedral_angle_3_deg	16.786
r_dihedral_angle_4_deg	14.757
r_dihedral_angle_1_deg	4.628
r_scangle_it	1.388
r_angle_refined_deg	1.06
r_scbond_it	0.781
r_mcangle_it	0.648
r_mcbond_it	0.363
r_nbtor_refined	0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.021
r_dihedral_angle_3_deg	16.786
r_dihedral_angle_4_deg	14.757
r_dihedral_angle_1_deg	4.628
r_scangle_it	1.388
r_angle_refined_deg	1.06
r_scbond_it	0.781
r_mcangle_it	0.648
r_mcbond_it	0.363
r_nbtor_refined	0.292
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.174
r_xyhbond_nbd_refined	0.136
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10184
Nucleic Acid Atoms	2805
Solvent Atoms	822
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	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.