9QP8 | pdb_00009qp8

Diels Alderase Cyc15b

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8OF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Sodium phosphate monobasic monohydrate, Potasium phosphate monobasic, Sodium HEPES

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.41	α = 90
b = 78.41	β = 90
c = 123.45	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	DECTRIS EIGER2 S 16M		2024-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.97	41.15	99.9	0.395	0.415	0.126	0.995	6.5	20.2		31669

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.97	2.02	99.6		7.523	7.917	2.458	0.324	0.4	19.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	2.2	41.15	22895	1130	99.878	0.198	0.1954	0.1955	0.2395	0.2394	36.244

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]
0.099	0.05		0.099		-0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.021
r_dihedral_angle_3_deg	14.168
r_dihedral_angle_2_deg	10.763
r_dihedral_angle_1_deg	8.096
r_lrange_it	7.575
r_scangle_it	6.554
r_scbond_it	5.06
r_mcangle_it	3.866
r_mcbond_it	2.785
r_angle_refined_deg	2.485
r_nbtor_refined	0.312
r_symmetry_xyhbond_nbd_refined	0.247
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.171
r_chiral_restr	0.164
r_xyhbond_nbd_refined	0.123
r_ncsr_local_group_1	0.119
r_bond_refined_d	0.015
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2092
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing