3B5P | pdb_00003b5p

Crystal structure of a cadd-like protein of unknown function (npun_f6505) from nostoc punctiforme pcc 73102 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 0.2M Mg(OAc)2, 20.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.67	α = 90
b = 78.51	β = 112.29
c = 45.58	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		2007-09-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0000, 0.9797, 0.9796	ALS	8.2.1

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	28.736	91.9	0.069	6.85			16846		-3	27.36

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	2.06	66		0.431	1.5

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	28.736	16827	851	98.24	0.169	0.167	0.17	0.225	0.23	RANDOM	24.038

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]
1.58		1.95	-1.19		1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.608
r_dihedral_angle_3_deg	14.666
r_dihedral_angle_4_deg	14.276
r_scangle_it	7.628
r_dihedral_angle_1_deg	6.143
r_scbond_it	5.972
r_mcangle_it	3.374
r_mcbond_it	2.34
r_angle_refined_deg	1.434
r_angle_other_deg	1.031
r_mcbond_other	0.584
r_symmetry_vdw_other	0.215
r_symmetry_hbond_refined	0.209
r_nbd_refined	0.206
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.173
r_nbd_other	0.169
r_symmetry_vdw_refined	0.105
r_chiral_restr	0.085
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1783
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing