5YHB

Crystal structure of Pd(allyl)/polyhedra mutant with deletion of Gly192-Ala194

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL		300	in vivo crystallization

Crystal Properties
Matthews coefficient	Solvent content
1.76	30.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.92	α = 90
b = 105.92	β = 90
c = 105.92	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2016-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1	SPring-8	BL32XU

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	2.08	50	100	0.908	0.994	9.78	68.9		12029

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	2.08	2.21	100		14.8	0.386	0.95	69.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GQK	2.08	43.2	10839	1190	99.98	0.19371	0.18824	0.24367	RANDOM	36.449

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.41
r_dihedral_angle_3_deg	18.523
r_dihedral_angle_4_deg	16.436
r_long_range_B_refined	7.501
r_long_range_B_other	7.457
r_dihedral_angle_1_deg	7.359
r_scangle_other	5.815
r_mcangle_other	4.087
r_mcangle_it	4.084
r_scbond_it	3.774
r_scbond_other	3.773
r_mcbond_it	2.713
r_mcbond_other	2.687
r_angle_refined_deg	1.762
r_angle_other_deg	1.114
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1459
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing