3E28 | pdb_00003e28

H. influenzae beta-carbonic anhydrase, variant Y181F

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A8D	PDB ENTRY 2A8D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.1 M Hepes, 1.5 M ammonium sulfate, 4% PEG-400, 20 mg/ml protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 230.193	α = 90
b = 144.943	β = 93.78
c = 52.714	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	IMAGE PLATE	RIGAKU RAXIS IV		2003-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.5	29.841	99.9	0.09	19.6	4		59536

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	2.5	2.64	100		0.52	2.6	4	8715

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 2A8D	2.5	29.84	59233	2984	99.47	0.208	0.206	0.211	0.256	0.2586	RANDOM	42.542

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		-0.1	-0.11		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.19
r_dihedral_angle_4_deg	20.628
r_dihedral_angle_3_deg	17.799
r_dihedral_angle_1_deg	6.672
r_scangle_it	1.941
r_scbond_it	1.331
r_angle_refined_deg	1.311
r_angle_other_deg	0.882
r_mcangle_it	0.773
r_mcbond_it	0.647
r_symmetry_hbond_refined	0.261
r_nbd_refined	0.223
r_symmetry_vdw_other	0.218
r_nbd_other	0.195
r_symmetry_vdw_refined	0.182
r_nbtor_refined	0.181
r_xyhbond_nbd_other	0.167
r_xyhbond_nbd_refined	0.165
r_mcbond_other	0.093
r_nbtor_other	0.089
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9874
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	86

Software

Software
Software Name	Purpose
SCALA	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling