3MX1 | pdb_00003mx1

The structure of GIY-YIG endonuclease R.Eco29kI

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		MAD, phase information by PHENIX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1M Tris HCl, 1.5M NaCl, 10% ethanol v/v, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.906	α = 90
b = 90.074	β = 90
c = 88.85	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315		2009-07-29	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315		2009-10-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0	ALS	5.0.1
2	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9801, 0.9802, 0.975	ALS	5.0.2

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	2.3	62.91	98.82	0.079	18.35	4.9	15893	15078

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)
	2.3	2.358	94.2		0.311	4.2	4.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	Phase information by PHENIX	2.3	50	15893	15078	791	98.82	0.18507	0.18285	0.2	0.22781	0.25	RANDOM	42.06

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]
0.62			1.97		-2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.557
r_dihedral_angle_3_deg	15.522
r_dihedral_angle_4_deg	14.827
r_dihedral_angle_1_deg	7.659
r_scangle_it	5.291
r_scbond_it	3.38
r_mcangle_it	2.346
r_angle_refined_deg	1.951
r_mcbond_it	1.279
r_chiral_restr	0.139
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1640
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing