7LB9 | pdb_00007lb9

Pseudomonas fluorescens G150T isocyanide hydratase (G150T-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	6NI4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	298	25% PEG 3350, 200 MM MAGNESIUM CHLORIDE, 100MM TRIS-HCL, PH 8.6, 2 MM Dithiothreitol

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.295	α = 90
b = 59.716	β = 110.876
c = 69.505	γ = 90

Symmetry
Space Group	I 1 2 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	1.101	35.222	95.7	0.057	0.998	11.8	3.6		82868

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	1.101	1.12	93.4		1.839	0.334	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	6ni4	1.101	35.222	82864	2457	95.293	0.127	0.1267	0.13	0.1406	0.14	random	16.172

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]
0.061		-0.113	0.131		-0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.084
r_dihedral_angle_4_deg	14.004
r_dihedral_angle_3_deg	12.204
r_rigid_bond_restr	11.407
r_dihedral_angle_1_deg	5.819
r_lrange_it	2.863
r_lrange_other	2.595
r_scangle_it	2.285
r_scangle_other	2.285
r_angle_other_deg	2.254
r_scbond_other	1.767
r_scbond_it	1.765
r_mcangle_it	1.564
r_mcangle_other	1.564
r_angle_refined_deg	1.466
r_mcbond_it	1.183
r_mcbond_other	1.183
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.211
r_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_other	0.159
r_symmetry_nbd_refined	0.155
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.067
r_bond_other_d	0.035
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1673
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms

Software

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