1YD6 | pdb_00001yd6

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Bacillus caldotenax

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	295	Ammonium Sulfate, DTT, Sodium Acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.487	α = 90
b = 86.66	β = 120.16
c = 67.862	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		2003-01-01	M	MAD
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.0	NSLS	X26C
2	SYNCHROTRON	NSLS BEAMLINE X12B	1.0	NSLS	X12B
3	SYNCHROTRON	NSLS BEAMLINE X25	1.0	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	30	100			29029	29029	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.08	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MAD	THROUGHOUT	2	15	2	27724	27724	1487	100	0.219	0.20496	0.2024	0.21	0.25203	0.26	RANDOM	36.111

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]
-0.43		-2.24	0.83		-2.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.154
r_dihedral_angle_4_deg	17.4
r_dihedral_angle_3_deg	15.875
r_dihedral_angle_1_deg	5.218
r_scangle_it	3.383
r_scbond_it	2.303
r_mcangle_it	1.675
r_angle_refined_deg	1.508
r_mcbond_it	1.062
r_angle_other_deg	0.869
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.212
r_mcbond_other	0.21
r_symmetry_vdw_other	0.207
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.177
r_symmetry_hbond_refined	0.151
r_chiral_restr	0.107
r_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2966
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing