7YCD | pdb_00007ycd

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis bound with (R)-(+)-ALPHA-HYDROXYBENZENE-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, 2.0 M ammonium sulfate, incubated in 25% (v/v) glycerol with a drop of BA and 2M potassium cyanide

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.43	α = 90
b = 123.43	β = 90
c = 129.87	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	64.94	99.5	0.066	8.2	3.1		74395

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			0.846

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	40.435	74350	3640	99.458	0.203	0.2019	0.21	0.233	0.24	42.59

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]
0.782	0.391		0.782		-2.538

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.159
r_dihedral_angle_3_deg	15.716
r_dihedral_angle_2_deg	10.262
r_lrange_it	7.748
r_lrange_other	7.725
r_dihedral_angle_1_deg	7.666
r_scangle_it	6.368
r_scangle_other	6.171
r_mcangle_it	4.751
r_mcangle_other	4.751
r_scbond_it	4.537
r_scbond_other	4.337
r_mcbond_it	3.501
r_mcbond_other	3.501
r_angle_refined_deg	1.546
r_angle_other_deg	0.526
r_nbd_refined	0.215
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.191
r_nbd_other	0.184
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.1
r_symmetry_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_refined	0.078
r_chiral_restr	0.069
r_chiral_restr_other	0.02
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5058
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	110

Software

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