7TNB | pdb_00007tnb

Caulobacter segnis arene reductase (CSAR) - WT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MYW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	Crystal Screen #20: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000 Protein dissolved in 100 mM KPi, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.47	α = 90
b = 104.175	β = 90
c = 144.328	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	100	PIXEL	DECTRIS EIGER X 9M		2018-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-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	1.79	29.68	99.8	0.147	0.159	0.06	0.998	12.9	13.3		33499

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	1.79	1.83	97.3		1.39	1.513	0.589	0.745

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6MYW	1.79	29.678	33460	1663	99.827	0.155	0.1531	0.17	0.1859	0.2	18.671

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]
-1.436			2.188		-0.752

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.065
r_dihedral_angle_4_deg	17.07
r_dihedral_angle_3_deg	13.373
r_dihedral_angle_1_deg	7.026
r_lrange_it	5.15
r_lrange_other	4.959
r_scangle_it	4.024
r_scangle_other	3.913
r_scbond_it	2.867
r_scbond_other	2.767
r_mcangle_it	1.797
r_mcangle_other	1.797
r_angle_refined_deg	1.592
r_angle_other_deg	1.464
r_mcbond_it	1.34
r_mcbond_other	1.313
r_symmetry_xyhbond_nbd_refined	0.329
r_symmetry_nbd_refined	0.245
r_nbd_refined	0.204
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.168
r_nbd_other	0.165
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2651
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	82

Software

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