7YCT | pdb_00007yct

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis complexed with (R)-2-Chloromandelonitrile

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1 M BIS-TRIS (pH 5.5), 2.0 M ammonium sulfate incubated in 25% (v/v) glycerol with a drop of (R)-2-Chlorobenzaldehyde, and soaked with 2 M potassium cyanide

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.79	α = 90
b = 123.79	β = 90
c = 129.5	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	293.15	IMAGE PLATE	RIGAKU		2017-08-16	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	61.9	99.2	0.052	10.4	3		74391

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			0.294

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	53.66	74380	3627	99.21	0.172	0.171	0.18	0.1996	0.21	29.239

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]
0.007	0.004		0.007		-0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.829
r_dihedral_angle_3_deg	15.095
r_dihedral_angle_2_deg	10.387
r_dihedral_angle_1_deg	7.708
r_lrange_it	7.662
r_lrange_other	7.581
r_scangle_it	6.149
r_scangle_other	5.973
r_scbond_it	4.497
r_scbond_other	4.326
r_mcangle_it	3.76
r_mcangle_other	3.759
r_mcbond_it	2.83
r_mcbond_other	2.829
r_angle_refined_deg	1.692
r_angle_other_deg	0.575
r_nbd_refined	0.225
r_symmetry_nbd_other	0.199
r_symmetry_xyhbond_nbd_other	0.198
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.128
r_nbd_other	0.122
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.08
r_symmetry_nbd_refined	0.066
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	5055
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	121

Software

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