2IKB | pdb_00002ikb

Crystal Structure of a Protein of Unknown Function NMB1012 from Neisseria meningitidis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	20% w/v PEG MME2000, 0.1M Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.335	α = 90
b = 52.087	β = 90.68
c = 128.874	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 QUANTUM 315	mirrors	2006-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97980	APS	19-ID

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	1.7	50	98.63	0.105	15.3	4.8	65867	64965		2	20.1

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	1.7	1.744	93.61		0.371	2.47	4.2	5132

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.7	38.38	64965	64965	3482	98.63	0.19717	0.19717	0.19455	0.2093	0.247	0.2589	RANDOM	20.192

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]
1.11		-1.11	-1.89		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.571
r_dihedral_angle_4_deg	16.135
r_dihedral_angle_3_deg	13.961
r_dihedral_angle_1_deg	5.929
r_scangle_it	3.416
r_scbond_it	2.467
r_mcangle_it	1.5
r_angle_refined_deg	1.41
r_mcbond_it	1.285
r_angle_other_deg	0.973
r_symmetry_vdw_other	0.297
r_mcbond_other	0.266
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.236
r_nbd_other	0.203
r_nbtor_refined	0.189
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.151
r_nbtor_other	0.085
r_chiral_restr	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5067
Nucleic Acid Atoms
Solvent Atoms	557
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building