7LA0 | pdb_00007la0

Pseudomonas fluorescens G150A isocyanide hydratase (G150A-2) at 274K, Refmac5-refined

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6NI5

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
2.2	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.155	α = 90
b = 57.87	β = 112.744
c = 68.988	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	1.25	39	95.6	0.071	0.998	7	3		109380

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	1.25	1.27	90.1		1.851	0.317	0.8	2.9

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	6NI5	1.25	38.999	108127	3309	94.281	0.125	0.1237	0.13	0.1524	0.15	random	18.185

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]
-0.159		0.09	-0.288		0.275

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.531
r_dihedral_angle_4_deg	19.875
r_dihedral_angle_3_deg	12.782
r_dihedral_angle_1_deg	6.271
r_lrange_it	3.302
r_lrange_other	3.109
r_scangle_it	2.78
r_scangle_other	2.779
r_scbond_it	2.217
r_scbond_other	2.217
r_mcangle_other	1.922
r_mcangle_it	1.919
r_rigid_bond_restr	1.606
r_mcbond_it	1.512
r_mcbond_other	1.498
r_angle_refined_deg	1.473
r_angle_other_deg	1.442
r_symmetry_xyhbond_nbd_other	0.366
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.204
r_nbd_other	0.202
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.111
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.078
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	3374
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms

Software

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