7L9Q | pdb_00007l9q

Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at 274K, Refmac5-refined

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6NI6	PDB entry 6NI6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	298	23% PEG3350, 100 mM Tris-HCl, pH 8.6, 200 mM magnesium chloride, 2 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.305	α = 90
b = 58.188	β = 112.808
c = 69.015	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	274	PIXEL	DECTRIS PILATUS 6M	FLAT SI RH COATED M0, KIRKPATRICK-BAEZ FLAT BENT SI M1 & M2	2019-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.775	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.149	39.142	93.5	0.058	0.999	12.9	3.9		138486

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.149	1.17	89.3		1.28	0.483	1.4	3.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 6NI6	1.149	39.142	138457	4137	93.25	0.122	0.1209	0.12	0.144	0.15	random	16.871

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]
0.024		0.107	-0.04		-0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.628
r_dihedral_angle_4_deg	17.836
r_dihedral_angle_3_deg	11.889
r_dihedral_angle_1_deg	6.105
r_lrange_it	2.811
r_lrange_other	2.592
r_scangle_it	2.256
r_scangle_other	2.256
r_scbond_it	1.774
r_scbond_other	1.774
r_mcangle_other	1.523
r_mcangle_it	1.521
r_angle_refined_deg	1.493
r_angle_other_deg	1.491
r_rigid_bond_restr	1.296
r_mcbond_it	1.176
r_mcbond_other	1.168
r_nbd_refined	0.227
r_nbd_other	0.217
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.119
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3368
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms

Software

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