5H83 | pdb_00005h83

HETEROYOHIMBINE SYNTHASE HYS FROM CATHARANTHUS ROSEUS - APO FORM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FI3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	NULL

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.63	α = 90
b = 188.63	β = 90
c = 58.95	γ = 90

Symmetry
Space Group	I 4

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 PILATUS3 6M		2015-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.25	48.32	99.7	0.14	0.068	0.996	9.1	5.1		49387			31.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	97.8		1.366	0.664	0.51	1.1	5	3545

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5FI3	2.25	48.32	46849	2536	99.63	0.192	0.1902	0.1992	0.2242	0.2269	RANDOM	52.8

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]
1.8			1.8		-3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.795
r_dihedral_angle_3_deg	13.687
r_dihedral_angle_4_deg	13.656
r_dihedral_angle_1_deg	6.595
r_mcangle_it	4.359
r_mcbond_it	3.208
r_mcbond_other	3.208
r_angle_refined_deg	1.416
r_angle_other_deg	0.953
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5217
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction