2DPH | pdb_00002dph

Crystal Structure of Formaldehyde dismutase

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.229	α = 90
b = 90.229	β = 90
c = 226.689	γ = 90

Symmetry
Space Group	I 41

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 QUANTUM 4		2002-02-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.2736, 1.2832, 1.2827	SPring-8	BL38B1

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	2.27	41.92	99.8	0.059	8.7	3.77	41645	41519

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	2.27	2.35	99.3		0.201	3	3.33

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.27	41.92	39428	2085	100	0.209	0.207	0.21	0.25	0.25	RANDOM	31.09

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]
0.82			0.82		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.862
r_dihedral_angle_3_deg	14.896
r_dihedral_angle_4_deg	14.641
r_dihedral_angle_1_deg	6.177
r_scangle_it	1.895
r_angle_refined_deg	1.273
r_scbond_it	1.241
r_mcangle_it	0.794
r_mcbond_it	0.458
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.185
r_symmetry_hbond_refined	0.14
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.081
r_metal_ion_refined	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6016
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling
MLPHARE	phasing