7L9S | pdb_00007l9s

Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-2) 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
2.22	44.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.297	α = 90
b = 58.215	β = 112.825
c = 69.052	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	2018-11-28	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	1.2	38.672	97.4	0.068	0.998	6.8	2.7		127238

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	1.2	1.22	94.3		1.768	0.257	0.8	2.5

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	1.2	38.672	127216	3838	97.25	0.124	0.1234	0.12	0.1523	0.15	random	16.837

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]
0.04		-0.137	0.339		-0.195

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.444
r_dihedral_angle_4_deg	19.148
r_dihedral_angle_3_deg	12.012
r_dihedral_angle_1_deg	6.043
r_lrange_it	3.119
r_lrange_other	2.85
r_scangle_it	2.614
r_scangle_other	2.614
r_scbond_it	2.136
r_scbond_other	2.135
r_mcangle_other	1.729
r_mcangle_it	1.728
r_rigid_bond_restr	1.528
r_angle_refined_deg	1.52
r_angle_other_deg	1.486
r_mcbond_it	1.331
r_mcbond_other	1.323
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.202
r_symmetry_nbd_other	0.175
r_symmetry_nbd_refined	0.172
r_nbd_other	0.166
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_other	0.095
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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	366
Heterogen Atoms

Software

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