1UMP | pdb_00001ump

GEOMETRY OF TRITERPENE CONVERSION TO PENTACARBOCYCLIC HOPENE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GSZ	PDB ENTRY 1GSZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8		HANGING DROP WITH 5-8 MG/ML PROTEIN,0.3 PERCENT (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 PERCENT (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN RESPECT TO PROTEIN) 2-AZASQUALENE IN THE STARTING DROPLET. RESERVOIR CONTAINED 100 MM SODIUM CITRATE (PH 4.8), 100 MM SODIUM CHLORIDE, 6-16 PERCENT (V/V) PEG-600.

Crystal Properties
Matthews coefficient	Solvent content
2.94	57.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.144	α = 90
b = 139.144	β = 90
c = 240.699	γ = 120

Symmetry
Space Group	P 32 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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		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	2.13	20	99.4	0.052	18.2	5.5		149921

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	2.13	2.19	99.9		0.285	4.9	4.5

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	PDB ENTRY 1GSZ	2.13	19.73	146229	3691	100	0.187	0.186	0.2	0.228	0.24	RANDOM	23.79

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]
-1.14	-0.57		-1.14		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.694
r_scangle_it	2.647
r_scbond_it	1.666
r_angle_refined_deg	1.317
r_mcangle_it	0.933
r_angle_other_deg	0.853
r_mcbond_it	0.519
r_symmetry_hbond_refined	0.285
r_symmetry_vdw_refined	0.274
r_symmetry_vdw_other	0.233
r_nbd_other	0.231
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.203
r_nbtor_other	0.084
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14892
Nucleic Acid Atoms
Solvent Atoms	1210
Heterogen Atoms	195

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing