7YCF | pdb_00007ycf

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis IN ACETONITRILE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293.15	0.1 M BIS-TRIS containing 2.0 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.11	α = 90
b = 123.11	β = 90
c = 129.59	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU		2017-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.01	61.56	99.4	0.055	10.6	3.1		73724

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.05			0.302

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6KFE	2.01	53.365	73708	3594	99.362	0.174	0.1729	0.18	0.2028	0.21	31.328

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]
0.611	0.305		0.611		-1.981

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.953
r_dihedral_angle_3_deg	15.264
r_dihedral_angle_2_deg	14.881
r_dihedral_angle_1_deg	7.745
r_lrange_it	7.555
r_lrange_other	7.424
r_scangle_it	6.172
r_scangle_other	5.913
r_scbond_it	4.546
r_scbond_other	4.12
r_mcangle_it	3.901
r_mcangle_other	3.901
r_mcbond_it	2.949
r_mcbond_other	2.949
r_angle_refined_deg	1.69
r_angle_other_deg	0.564
r_symmetry_xyhbond_nbd_other	0.339
r_nbd_refined	0.22
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.144
r_nbd_other	0.134
r_symmetry_nbd_refined	0.121
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5072
Nucleic Acid Atoms
Solvent Atoms	350
Heterogen Atoms	145

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
Coot	model building