4MC3 | pdb_00004mc3

Hedycaryol synthase in complex with Nerolidol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Hedycaryol Synthase experimentally phased with HgCl2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	4M Sodium formiate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.44	α = 90
b = 59.44	β = 90
c = 182.84	γ = 120

Symmetry
Space Group	P 31 2 1

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	PSI PILATUS 6M		2012-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	1.5	44.855	98.4	0.043	20.4	6.4	62111	61118	2	2

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	1.5	1.6	96.8		0.548	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Hedycaryol Synthase experimentally phased with HgCl2	1.5	44.855	60116	57110	3006	98.35	0.14549	0.14324	0.15	0.18922	0.2	RANDOM	33.987

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]
0.43	0.43		0.43		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.464
r_sphericity_free	31.898
r_dihedral_angle_4_deg	20.121
r_dihedral_angle_3_deg	12.919
r_sphericity_bonded	11.881
r_rigid_bond_restr	4.535
r_dihedral_angle_1_deg	4.384
r_angle_refined_deg	1.613
r_angle_other_deg	1.087
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2267
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	16

Software

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