7QVB | pdb_00007qvb

Crystal structure of the DNA-binding protein DdrC from Deinococcus radiodurans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.1 M Tris pH8.0, 1.2 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.721	α = 90
b = 111.721	β = 90
c = 105.187	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	PIXEL	DECTRIS PILATUS3 2M		2018-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9660	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.5	49.34	99.9	0.084	0.099	0.051	0.999	12.6	6.4		26653			60.08

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	99.8		2.012	2.368	1.219	0.479	1.1	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.5	46.251	26627	1333	99.753	0.186	0.1827	0.19	0.2465	0.25	Random selection	75.241

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]
-1.649	-0.824		-1.649		5.348

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.197
r_dihedral_angle_3_deg	14.243
r_dihedral_angle_4_deg	13.973
r_lrange_it	6.913
r_lrange_other	6.894
r_scangle_it	6.529
r_scangle_other	5.351
r_mcangle_it	5.304
r_mcangle_other	5.303
r_dihedral_angle_1_deg	4.824
r_scbond_it	4.615
r_scbond_other	3.861
r_mcbond_other	3.785
r_mcbond_it	3.784
r_angle_refined_deg	1.233
r_angle_other_deg	1.132
r_rigid_bond_restr	0.877
r_nbd_other	0.237
r_symmetry_xyhbond_nbd_refined	0.23
r_symmetry_nbd_refined	0.227
r_nbd_refined	0.179
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.138
r_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.046
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3368
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
PHASER	phasing
XDS	data scaling
XDS	data reduction