2W2K

Crystal structure of the apo forms of Rhodotorula graminis D- mandelate dehydrogenase at 1.8A.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MX3	PDB ENTRY 1MX3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		100 MM MES-NAOH PH 6.0, 200 MM NACL, 20% PEG-MME5K, 1% DIOXANE, 1MM DTT.

Crystal Properties
Matthews coefficient	Solvent content
2.49	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.03	α = 90
b = 81.071	β = 96.27
c = 93.955	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	100	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6		SRS	PX9.6

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	1.8	29.8	95.1	0.05	0.2	2.4		59834		2	14.6

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	1.85	1.95	88.4		0.09	9	2.3

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	PDB ENTRY 1MX3	1.85	25.96	56812	3020	100	0.156	0.154	0.15	0.199	0.2	RANDOM	15.12

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]
0.06		-0.11	-0.07		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.326
r_dihedral_angle_4_deg	15.33
r_dihedral_angle_3_deg	12.019
r_dihedral_angle_1_deg	6.03
r_scangle_it	5.349
r_scbond_it	4.154
r_mcangle_it	2.624
r_mcbond_it	2.068
r_angle_refined_deg	1.329
r_nbtor_refined	0.285
r_nbd_refined	0.184
r_xyhbond_nbd_refined	0.128
r_symmetry_vdw_refined	0.127
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.093
r_bond_refined_d	0.019
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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	5304
Nucleic Acid Atoms
Solvent Atoms	741
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
PHASER	phasing