5HBQ

C63D mutant of the rhodanese domain of YgaP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	0.2 M sodium acetate in 0.1 M Tris HCl pH 8.5, and 30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.896	α = 90
b = 43.896	β = 90
c = 52.667	γ = 120

Symmetry
Space Group	P 31

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 315r		2013-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	1.127	SSRL	BL12-2

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	1.66	38	99.6	0.068	15.3	5.2		13404

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	1.66	1.75	98		0.67	2	4	1947

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	5HBL	1.66	38	12627	658	98.85	0.18742	0.18572	0.22252	RANDOM	19.07

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]
-2.49			-2.49		4.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.984
r_dihedral_angle_3_deg	13.806
r_dihedral_angle_4_deg	12.419
r_dihedral_angle_1_deg	5.879
r_long_range_B_refined	4.559
r_long_range_B_other	4.341
r_scangle_other	2.341
r_mcangle_it	1.673
r_mcangle_other	1.673
r_angle_refined_deg	1.579
r_scbond_it	1.489
r_scbond_other	1.487
r_mcbond_it	1.128
r_mcbond_other	1.123
r_angle_other_deg	0.994
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	789
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing