7L9W | pdb_00007l9w

Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-3) 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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	298	23% PEG 3350, 100MM TRIS-HCL PH 8.6, 200 MM MAGNESIUM CHLORIDE AND 2 MM DITHIOTHREITOL

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.31	α = 90
b = 58.215	β = 112.811
c = 69.03	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	1.199	39.152	96.5	0.069	0.997	7.1	3.7		126107

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	1.199	1.22	91.9		1.737	0.309	1.1	3.5

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	6NI6	1.199	39.152	126085	3768	96.351	0.125	0.1244	0.13	0.151	0.15	random	17.448

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]
0.134		0.215	-0.469		0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.695
r_dihedral_angle_4_deg	18.281
r_dihedral_angle_3_deg	11.887
r_dihedral_angle_1_deg	6.025
r_lrange_it	3.142
r_lrange_other	2.863
r_scangle_it	2.636
r_scangle_other	2.636
r_scbond_it	2.104
r_scbond_other	2.104
r_mcangle_other	1.745
r_mcangle_it	1.743
r_rigid_bond_restr	1.612
r_angle_refined_deg	1.529
r_angle_other_deg	1.489
r_mcbond_it	1.408
r_mcbond_other	1.399
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.191
r_nbd_other	0.185
r_symmetry_nbd_other	0.181
r_symmetry_xyhbond_nbd_other	0.177
r_symmetry_nbd_refined	0.165
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.145
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3368
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms

Software

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