9RCR | pdb_00009rcr

1,2-propanediol dehydratase with 0.1 % 1,2-propanediol additive

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.6 M ammonium acetate, 4% PEG 4000, 0.1 M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.89	α = 90
b = 199.973	β = 106.323
c = 118.377	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS EIGER2 XE 16M		2025-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95374	Diamond	I04

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	2.8	98.78	97.3	0.858	1.03	0.561	0.3	4.3	6.3		86164			35.67

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	2.8	2.85	92.9		5.835	11.338	4.087	0.192	1.2	5.4

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	2.8	98.7	85965	4009	97.074	0.265	0.2626	0.2581	0.3178	0.3131	26.739

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]
1.912		1.34	-2.38		-0.271

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.623
r_dihedral_angle_4_deg	19.099
r_dihedral_angle_3_deg	15.81
r_dihedral_angle_1_deg	7.578
r_lrange_it	3.642
r_lrange_other	3.642
r_scangle_it	2.779
r_scangle_other	2.779
r_mcangle_it	2.438
r_mcangle_other	2.438
r_scbond_it	1.886
r_scbond_other	1.886
r_mcbond_it	1.571
r_mcbond_other	1.57
r_angle_other_deg	1.51
r_angle_refined_deg	1.328
r_symmetry_xyhbond_nbd_refined	0.33
r_nbd_other	0.325
r_symmetry_nbd_refined	0.282
r_symmetry_nbd_other	0.219
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_other	0.094
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.072
r_bond_other_d	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25001
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	15

Software

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