9GBG | pdb_00009gbg

Putative Phage Recombinase UvsX

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Z3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.7 mg/mL protein solution (in 20 mM HEPES pH 7.5, 300 mM NaCl) combined with 0.12 M Monosaccharides, 0.1 M Buffer System 3 (pH 8.5), 30 % v/v Precipitant Mix 2 (MORPHEUS screen, Molecular Dimensions Inc.).

Crystal Properties
Matthews coefficient	Solvent content
3.24	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.751	α = 90
b = 116.751	β = 90
c = 60.909	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	273	PIXEL	DECTRIS EIGER2 XE 16M		2020-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.970902	Diamond	I03

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	2.596	101.11	99.7	0.059	0.061	0.016	1	23.6	15		14778

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	2.6	2.71	97.6		1.045	1.081	0.275	0.902	2.7	15

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.596	101.109	14757	727	99.696	0.26	0.2577	0.2695	0.3064	0.3164	95.564

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]
-1.831	-0.916		-1.831		5.941

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.423
r_lrange_it	14.793
r_lrange_other	14.791
r_dihedral_angle_6_deg	14.707
r_scangle_it	12.968
r_scangle_other	12.962
r_mcangle_it	12.431
r_mcangle_other	12.43
r_scbond_it	10.612
r_scbond_other	10.605
r_mcbond_it	10.208
r_mcbond_other	10.149
r_dihedral_angle_1_deg	8.568
r_dihedral_angle_2_deg	5.277
r_angle_refined_deg	1.766
r_angle_other_deg	0.669
r_nbd_refined	0.263
r_symmetry_nbd_refined	0.231
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.169
r_nbd_other	0.129
r_symmetry_nbtor_other	0.107
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.078
r_symmetry_xyhbond_nbd_refined	0.05
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1845
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing