5XN8 | pdb_00005xn8

Structure of glycerol dehydrogenase crystallised as a contaminant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MCA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	295	0.1 M HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), pH 7.5, 0.02 M magnesium chloride hexahydrate

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.55	α = 90
b = 178.55	β = 90
c = 80.09	γ = 90

Symmetry
Space Group	P 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	IMAGE PLATE	MARRESEARCH		2014-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.33	56.46	89.3	0.2	0.98	8.07	6.8		96487

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.33	2.39	51.9		0.37	0.64		1.3

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	4MCA	2.33	56.46	91655	4831	89.31	0.23676	0.23598	0.24	0.25146	0.25	RANDOM	33.661

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]
9.29			9.29		-18.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.946
r_dihedral_angle_4_deg	18.69
r_dihedral_angle_3_deg	14.351
r_dihedral_angle_1_deg	5.541
r_long_range_B_refined	2.677
r_long_range_B_other	2.66
r_mcangle_it	1.522
r_mcangle_other	1.522
r_scangle_other	1.395
r_angle_refined_deg	1.198
r_mcbond_it	0.94
r_mcbond_other	0.94
r_angle_other_deg	0.912
r_scbond_it	0.877
r_scbond_other	0.875
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10932
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data processing
PHASER	phasing