7YCB | pdb_00007ycb

HYDROXYNITRILE LYASE FROM THE MILLIPEDE

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% glycerol with a drop of benzaldehyde and 2 M potassium cyanide

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.16	α = 90
b = 123.16	β = 90
c = 130.14	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	61.58	99.9	0.069	7.9	3		74529

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			0.069

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	49.396	74513	3631	99.893	0.208	0.2061	0.21	0.2349	0.24	39.04

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]
0.323	0.162		0.323		-1.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.57
r_dihedral_angle_3_deg	14.696
r_dihedral_angle_2_deg	10.637
r_dihedral_angle_1_deg	7.923
r_lrange_other	7.827
r_lrange_it	7.824
r_scangle_it	6.165
r_scangle_other	5.907
r_mcangle_it	4.807
r_mcangle_other	4.806
r_scbond_it	4.63
r_scbond_other	4.25
r_mcbond_it	3.503
r_mcbond_other	3.502
r_angle_refined_deg	1.541
r_angle_other_deg	0.514
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.219
r_symmetry_xyhbond_nbd_other	0.216
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.149
r_nbd_other	0.148
r_symmetry_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.069
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	5072
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	125

Software

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