2F46 | pdb_00002f46

Crystal structure of a putative phosphatase (nma1982) from neisseria meningitidis z2491 at 1.41 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8.5	277	0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.006356	38.694843

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.278	α = 90
b = 33.466	β = 96.18
c = 59.899	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 210	COLLIMATING MIRROR, DCM, TOROIDAL FOCUSING MIRROR	2005-10-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.019951, 0.979741	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.41	18.62	83.4	0.041	0.041	9	3.1		46247

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.41	1.45	32.3	32.3	0.276	0.276	2.5	1.6

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-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	1.41	18.62	43885	2352	83.43	0.201	0.20104	0.2	0.21	0.228	0.24	RANDOM	14.814

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]
-0.29		-0.39	0.32		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.039
r_dihedral_angle_4_deg	12.222
r_dihedral_angle_3_deg	12.054
r_scangle_it	6.447
r_dihedral_angle_1_deg	6.128
r_scbond_it	4.587
r_mcangle_it	2.903
r_mcbond_it	1.959
r_angle_refined_deg	1.452
r_angle_other_deg	0.837
r_mcbond_other	0.502
r_symmetry_vdw_other	0.307
r_symmetry_vdw_refined	0.29
r_nbd_refined	0.262
r_nbd_other	0.195
r_symmetry_hbond_refined	0.182
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.175
r_nbtor_other	0.083
r_chiral_restr	0.079
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2239
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing